Scientific Software in the MGCF

The workstations in 175 Tan Hall are named: gravel, betty, wilma, stone, bambam, slate, lava, bronto, bobcat, lynx and the Kavli funded machines: energy and nano. These all share the same software with a few rare exceptions.

The computing cluster is called Tiger and has 36 cpu nodes. Each node has 64 core and 512GB RAM. There are an additional 30 nodes each with 12 core and 48GB RAM per node. The total is 2664 available cpu cores averaging 8GB RAM per core. There is also a GPU node with 8 Nvida Tesla cards (= 30400 gpu core).

Tiger is managed by a queueing system and is not for interactive use. There are shortcut commands for many common programs to automate submission to the queue. These shortcut commands are specified in the individual software descriptions below. If that is not enough information, then try the FAQS and/or ask for help.

The notes below refer to software as available on 1) MGCF workstations or 2) Tiger (the computing cluster).


ADF

is a DFT program which can be applied to isolated molecules, polymers, slabs, solids, etc. It has relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei. Bond energy decomposition, fragment orbitals and charge decomposition options are available. QM/MM enables the treatment of many thousands of atoms. ADF includes meta-GGA and hybrid exchange-correlation functionals.

Due to lack of recent demand, we have temporarily allowed the license to expire. Please let us know if you want to use this software in your research so we can update the license and enable your access. We have some basic notes which you should read prior to using ADF.

The main adf program should be run on Tiger but the GUI is available on the MGCF workstations. To run the GUI, on and MGCF workstation command line, type
adf_setup
to set environment variables for that session.
Then type
adfinput
to start the graphical user interface. Use this to setup and then "Save As" your input files.
ADF generates a series of files with non-unique names so each ADF job should be run from its own folder. Make a folder for the calculation and move the input files to that folder.

On the command line, type
cd foldername
where foldername is the folder name with input files.
run_adf (not currently available)
to start your job in the queue on Tiger.

See the support page for documentation and examples.


Aimall

performs quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems, starting from molecular wavefunction data. It uses the method by Richard Bader of McMaster University of dividing molecules into atoms based on the electronic charge density.

Type aimstudio to start the graphical user interface. This is licensed only on the MGCF workstations named lynx and bobcat.

See the home page for more information including how to run calculations in batch mode. We also have the related program bader from University of Texas.


Amber 18 + Amber Tools

is a suite of molecular simulation programs used mostly for molecular dynamics of biomolecules. Major programs are:
sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived restraints, chemical shifts and NOESY volumes. Sander is also used for general molecular dynamics simulations, replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. Sander includes QM/MM capability.
pmemd: a modified version of the sander program, optimized for periodic, PME simulations, and for GB simulations. It is faster and scales better on parallel machines.
nmode: Normal mode analysis using first and second derivatives, used to search for local minima and transition states and perform vibrational analysis.
LEaP: an X-windows-based program for basic model building and Amber coordinate and parameter/topology input file creation.
antechamber: automates the process of developing force field descriptors for organic molecules. It generates files that can be read into LEaP.
cpptraj: is used to analyze MD trajectories.

The Amber home page has information and examples. To use xleap, etc on the workstations, type amber18_setup first. That sets environment variables for that shell. To run on Tiger, there are scripts to help:
For sander: run_amber and run_amber_gpu
For pmemd: run_pmemd and run_pmemd_gpu
These make basic job files which should be edited before submitting to the queue on Tiger. Ask MGCF staff for help.


APBS

performs a numerical solution of the Poisson-Boltzmann equation (PBE), a continuum model for electrostatic interactions between molecular solutes in salty, aqueous media. This is used in biomolecular simulation, including: simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent MD on biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants. APBS is enabled as a plugin in other programs but we maintain a command line version in case it is of use to you.

See the home page for usage instructions.

Type apbs_setup to activate APBS and related programs (pdb2pqr) for the current shell.
This program is on the MGCF workstations (not Tiger).


Art of Illusion

is an open source 3D modelling and rendering studio. It can create high quality, photorealistic images and animations. For information and tutorials, see the home page.
AOI is installed on the MGCF workstations (not Tiger). Type aoi to start.


ASE

Atomic Simulation Environment (ASE) is python-based software for enhancing a wide variety of atomistic molecular calculations. It interfaces with numerous electronic-structure and other molecular simulation software packages. It includes, among many others, tools for setting up and running calculations, global structure optimizations, and molecular dynamics. See the ASE home page for details.

In our facility, ASE is installed within the MGCF pre-built materials, matsci, molmod and AID_framework Conda environments.

See our Conda environments section for how to activate.

AID_framework is a particular ASE branch that includes tools for Machine-Learning assisted transition state location, see https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.122.156001.


Avogadro

is free, open source, multiplatform molecule editor and visualizer. It can build molecules, crytallographic cells, super cells, and nanotubes. It can also set up inputs for a variety of popular quantum mechanical packages. See the home page for details.
Type avogadro to start. This program is on the MGCF workstations (not Tiger).


Babel

is a very useful file conversion program. It converts between most file types seen in computational chemistry software.
Type babel -H to see how to use it. See the home page for more information.


Bioinformatics tools

We have an ever growing and changing set of Bioinformatics tools. These include
Bedtools 2.26.0
Bioclipse
FastQC
Trim Galore!
FLASH
SAM Tools
CD-Hit: for clustering DNA/protein sequence data.

We have more tools but we add and update them faster than we change the web page. Email us if you want other tools. Also, these tools are not in your PATH by default. Type: bio_setup to activate these programs. Activation is for that shell only.

See also R/Bioconductor. Many of these tools are moving to Conda and we will stop supporting the stand alone versions when appropriate.


Castep

uses DFT to simulate properties of materials including energetics, structure at the atomic level, vibrational properties, electronic response properties etc. In particular it has a wide range of spectroscopic features that link directly to experiment, such as infra-red and Raman spectroscopies, NMR, and core level spectra. See http://www.castep.org for documentation and tutorials. See also the background theory.


We have a 2 licenses: The commercial license is via Materials Studio. In May 2020, we obtained an academic license.

To use the Academic version of Castep (version 19.11) on our cluster (Tiger), you must have a folder with a cell and param file. Then open a terminal for your MGCF account and type:
cd foldername
(where foldername is the folder name with the cell and other files). The calculation name will be derived from the foldername. Each calculation must be in a unique folder.

The Pseudopotential handling is slightly different from the commercial version. See the Pseudopotential FAQ for how to handle this in the academic version. A small set of potential files are included in our version and that folder will be searched for usp files. Otherwise put the desired potential files into the calculation folder or see the documentation for on demand creation of those files.

To submit a 1 core job, type: run_castep
To submit a multi core job (16 core in this example), type: run_castep 16

The default num_core (number of cores) is 1. For parallel jobs in shared memory, sensible values are: 1,4,8,16,32,64 but many calculations require a specific factor based on symmetry. If you need more than 64, please email us.

See also Optados for DOS calculations from Castep output.

To use the commercial version of Castep from Materials Studio 2020, we assume you are using Materials Studio on your own machine to set up the inputs. Copy the entire folder for the Castep inputs to your MGCF account from your own machine. That folder should contain the cell and related files. The folder name should be letters, numbers, _ and -. It should have no spaces or other characters like ) [ ? #,.
Then open a terminal for your MGCF account and type:
cd foldername
(where foldername is the folder name with the cell and other files). Each commercial Castep job uses a large number of our Materials Studio license tokens so you can't run many jobs at once. Please monitor any running jobs. qdel jobs that are not progressing since you will be wasting licenses and preventing other people from using them. There are no license limits on the academic version.

You don't need to include pseudopotential files since Materials Studio has built in ones.

For a 1 core job, type: run_castep20
To submit a multi core job (16 core in this example), type: run_castep20 16

Sensible values are: 1,4,8,16,32,64 but many calculations require a specific factor based on symmetry. If you need more than 64, please email us.

You can run very short jobs on the command line on the MGCF workstations (not Tiger). For example, you might want to test inputs.
To do this, type
cd foldername
(where foldername is the folder name with the cell and other files).
castep_setup
to activate the software for the current shell only. Then type
mpirun -n 4 castep.mpi seedname
(where seedname is the file prefix for the cell, param etc files).

If it dies, then use the screen output to debug your input. Otherwise open a second terminal and type top to see if it running. Press q to end top. If it runs okay for a few minutes then go back to the terminal where you typed mpirun -n 4 castep.mpi seedname and type Ctrl-C to kill the interactive run (this is a really old operating system thing where Ctrl-C meant kill long before it meant copy). You can then use run_castep to submit to Tiger.


CCP4

CCP4 is a collection of programs for macromolecular crystallography. It includes ccp4mg (a viewer), SHELX tools and Coot (Crystallographic Object-Oriented Toolkit).

It is on the MGCF workstations (not Tiger). Before using CCP4, you must type: ccp4_setup to activate these programs for the current shell.

Type ls /home/mgcf/software-ws/ccp4-7.0/bin to see the list of programs.
See the CCP4 page for documentation.

RAVE is a related set of programs from the Uppsala Software Factory. Look in /home/mgcf/software-ws/rave to see program names and sample files. These are also activated by ccp4_setup.


Cfour

Coupled-Cluster techniques for Computational Chemistry uses ab initio methods, especially those based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC). Excited electronic states and other "multireference" problems are possible using the equation-of-motion (EOM) CC techniques and can study open-shell systems when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. It includes analytic second derivatives for all CC approaches up to full CCSDT, NMR chemical shifts at MP and CC levels of theory, calculation of anharmonic force fields, relativistic corrections, corrections to the Born-Oppenheimer approximation at the CC level, nonadiabatic coupling within the EOM framework, and more.

See http://www.ccfour.de for documentation and tutorials. Each group should download and send in the license form before using.


Charmm

Chemistry at HARvard Macromolecular Mechanics. It is a molecular simulation program with broad application but primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. See the home page. Files and examples are in /usr/software/charmm on MGCF computers.

Type charmm_setup to configure the environment variables needed for Charmm. These settings are only for that one terminal session.

Email us if you want to use Charmm on Tiger. We can help you prepare job files for the queue.


Chemdraw

See our Chemdraw page.


Chemissian

Chemissian is a user-friendly program for analyzing electronic structure and preparing publication-quality orbital energy-level diagrams from HF or DFT wave functions. Chemissian can also display density maps, AO contributions to each MO and simulated UV-vis spectra (from excitation calculations). It can read output files from Gaussian 03 and 09, US-GAMESS and PC-GAMESS.i

This is Windows only and since the MGCF workstations are Linux based, see our Windows page for access and use information.

Chemissian is also available for purchase.

To use Chemissian with Gaussian output, you must first run a single-point calculation with the following route section:

#P functional/basis pop=full gfinput
If you already have a checkpoint file, copy that to a new name and make your input file read the wave function from that .chk file, using the keyword guess=(read,only). The resulting calculation should finish very quickly.


Chimera and ChimeraX

Chimera is a great molecular graphics program developed at UCSF. ChimeraX is the next gen version.

These can do interactive visualization and analysis of molecular structures and data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Chimera can make high-quality images and animations and is really good with volume data.

We are going to retain both versions until Chimera is fully obsolete. But for now we are not certain that all features are ported to ChimeraX. This software is installed on the MGCF workstations (not the computing cluster). Type chimerax or chimera to start and/or request us to put icons on your Desktop. Note that this does not work over a remote connection and we recommend you download (free) copies for your own computer.

See the Chimera site and the ChimeraX site.


Compilers and Libraries

We have many scientific, graphical, mathematical, etc libraries. Here are a small subset selected for emphasis. Email us if you need more information. Also, see the FAQS.

All MGCF machines have gfortran, gcc, g77, g++, and java. These are all in your PATH but some special versions are in /usr/software. Look there for other compilers, libraries and parallel tools. You may need to adjust the PATH or LD_LIBRARY_PATH for specific tasks.

We have many versions of the Intel compilers and the Math Kernel Library. See the documentation. Before using the Intel compilers, type intel to include these in your PATH. You must do this each time you open a shell or build it into your script. Usually the intel command sets the latest version of the compiler. If you want more version control, type
alias | grep intel
to see aliases to setup older compilers. (The "|" is the vertical bar above the \ key, not a letter.)
Do not edit your .bashrc file to make permanent environment variable changes because the workstations and server have different configurations. Environment variable changes should be localized to the specific script or shell.

OpenMPI and other parallel tools are on the cluster and on most workstations. If you use run_qchem, run_g16 and related scripts to submit calculations, the correct parallel environment will be put in the queue script. If you need help to configure your own queue script, see the FAQS and/or email us.


Comsol

Comsol can simulate 1D, 2D and 3D physical processes that can be described with partial differential equations.

The program is on the MGCF workstations for interactive use. Longer simulations can be run on Tiger. Ask us for the latest instructions on this.

We have 2 licenses types for Comsol. One is a Class Kit License (CKL) shared with a group in the Dept of Nuclear Engineering, and the other is a Research License (RL). The CKL is fully featured and allows for 25 simultaneous student users. It includes the modules: ComsolGUI, ACDC, Acoustics, Batteries and Fuel Cells, CADImport, CADReader, CFD, CHEM Reaction Engineering, Electrochemistry, HeatTransfer, LLExcel, LLMatlab, LLSolidworks, Microfluidics, NonLinearStructMaterials, Optimization, ParticleTracing, RayOptics, RF, StructuralMechanics, WaveOptics

The RL only allows 2 simultaneous research users. It has all of the same modules as the CKL but also has: Mems MultiBodyDynamics Semiconductor.

If you are using Comsol for class, start Comsol version 5.6 (updated Oct 2021) using the CKL by typing:
comsol
If you are using Comsol for research, start Comsol version 5.6 using the RL by typing:
comsol_rl
Recent older versions can be started with the commands comsol55, comsol55_rl, etc. Let us know if you need these older versions since they will eventually be deleted.

comsol -help
will show other options.

For more information, see the Comsol site.

To run Comsol on the command line, we have an advice document.


Cambridge Structural Database

The CSD (Cambridge Structural Database) is the world repository of small molecule crystal structures maintained by the Cambridge Crystallographic Data Centre. The CSD records bibliographic, chemical and crystallographic information for organic & metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction.

You can use the CSD at their web interface (from a berkeley.edu address) but searching via the Conquest program (below) is more robust. The latest version as of July 2020 is on the MGCF workstations (not Tiger). We have an MGCF tutorial and there are CSD documentation and tutorials.

The search program is called Conquest. Type conquest to start.

CSD includes Vista for data analysis. Isostar for studying nonbonded interactions in CSD and PDB databases. Our installation includes Mogul, Mercury and related tools.

This is licensed for all UC people so you can download and install the CSD for yourself if you use it a lot.


Datawarrior

DataWarrior combines dynamic graphical views, interactive filtering and chemical intelligence. Scatter plots, box plots, bar and pie charts visualize numerical or category data and show trends of scaffolds or compound substitution patterns. Chemical descriptors encode aspects of chemical structures, like the chemical graph, chemical functionality or 3D pharmacophore features. These allow for fundamentally different types of molecular similarity measures, which can be used in clustering, filters or custom views. DataWarrior supports enumeration of combinatorial libraries as the creation of evolutionary libraries. Data can be used for multidimensional scaling methods, self organizing maps and other machine learning approaches. See the home page. Files and examples are in /usr/software/datawarrior on MGCF workstations.


Desmond

An efficient Molecular Dynamics program to compute energies and forces for many standard fixed-charged force fields used in biomolecular simulations. Desmond is also compatible with polarizable force fields based on the Drude formalism. The program includes methods for thermostatting (Andersen, Nose-Hoover, Langevin) and barostatting (Berendsen, Martyna-Tobias-Klein, and Langevin). Membrane simulations (constant surface area and surface tension) and semi-isotropic and fully anisotropic pressure coupling schemes are also available.

Desmond is distributed by DE Shaw Research but is implemented as part of the Schrodinger software suite. The graphical interface for Desmond is Maestro. There is good documentation (from UC Berkeley IP addresses only) and we have a tutorial. Ask for help before submitting large jobs. We can help you use the cpu/gpu more efficently. See also: Notes on using Maestro via X2Go.


Dia

Dia is used to create diagrams such as entity relationship diagrams, UML diagrams, flowcharts, network diagrams, and simple circuits. One can add new shapes by writing simple XML files, using a subset of SVG to draw the shape. It can load and save diagrams in XML and other formats. For more information, see the Dia home page.

This is available on the MGCF workstations (not Tiger). Type dia to start.


Diamond

Diamond is a program for visualization and exploration of crystal structures. A full list of functions is here.

This is Windows only and since the MGCF workstations are Linux based, see our Windows page for access and use information.

The College of Chemistry has a site license. If you want a copy for yourself, email MGCF staff from your berkeley.edu address and state your College of Chemistry affiliation. We will then share the license file with you.

More information is on the home page.


DFTB+

DFTB+ is based on the Density Functional Tight Binding (DFTB) method giving quantum mechanical simulations in an approximate way gaining around two order of magnitude in speed. You can optimize the structure of molecules and solids, calculate one electron spectra, band structures, and electron transport under non-equilibrium conditions. More information is here.

Type: dftb_setup to activate this software for the current shell only. The program executable is dftb. The programs modes and waveplot are installed along with the dptools suite.

To submit jobs to Tiger, login in to any MGCF workstation, cd to the calculation folder (one calulation per folder is advised). Then type:
run_dftb+ num_core
The default num_core (number of cores) is 4. For parallel jobs in shared memory, Sensible values are: 1,4,8,16,32,64 but many DFTB+ calculations are sensitive to this, requiring a value which is a factor related to the calculation settings.
Slater-Koster files are in /usr/software/dftbplus-19.1/slakos/
Look in that folder and choose a subfolder for your SlaterKosterFiles Prefix.


DFT-D3

DFT-D3 is described in a JCP article. It calculates atom-pairwise dispersion corrections for noncovalent interactions for standard density functionals. This is a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

This is available on the MGCF workstations (not on the server). See the home page for usage information.
Type dftd3 to start.


Dock 6.1

Dock is as suite of programs to find favorable orientations of a ligand in a receptor. It is a command line driven program and output can be visualized in chimera. Users should read the manual and work the tutorials at the DOCK home page.

You will need to add the executables to your PATH before running. Email MGCF staff for help.


FEFF and JFEFF

Feff does ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS), X-ray Absorption Near-Edge Structure (XANES) and other spectra for clusters of atoms. The code yields scattering amplitudes and phases used in many modern XAFS analysis codes. Email us to configure your login if you want to use this. It runs on our MGCF workstations (not the server). We have version 9.6 revision 4. Jfeff is the GUI.


Gabedit

Gabedit is a graphical interface to chemistry packages such as Gamess, Gaussian, Molcas, Molpro, MPQC and Q-Chem. It is available from from Sourceforge. Note that we recommend IQmol as an interface for Q-Chem.

This software is on MGCF workstations. Type gabedit to start.


Gamess

GAMESS is a well known ab initio quantum chemistry program. See the Gamess home page and documentation. We also have the manuals on MGCF workstations in /usr/software/gamess/docs/

We have version Sept 30, 2019 R2 on the workstations and on the computing cluster (Tiger). Gamess is available on all MGCF linux machines but it should primarily be run on the computing cluster. Single core jobs can be run in the queue using:
run_gamess exam01
This will look for an input file called exam01.inp.

Memory allocation for a Gamess calculation is specified in the input file using the MWORDS keyword in the $SYSTEM group, which provides global control information for computer's operation.

$SYSTEM MWORDS=n $END

MWORDS specify memory for each processor, where n is an integral in units of 1,000,000 Words (1 Word = 8 Bytes). For example, if you want to allocate about 2GBytes of memory for each processor, use MWORDS=250. Use no more than MWORDS=400 per processor on Tiger.

Some parallel calculations require the grand total memory needed for the distributed data interface (DDI) storage. This can be specified by using the keyword MEMDDI. Please check Gamess input manual for details.

If you need to use more than 1 cpu , then the command is:
run_gamess exam01.inp [num_cpu]
The server architecture matters when choosing the number of cpus. Our nodes are 64 core in shared memory but very few calculations scale well enough to use all, so rational num_cpu choices for large systems are 16 and 32.

Very short jobs to test inputs may be run on the command line on the MGCF workstations (not Tiger). Type
gamess_setup
to activate the software for the current shell only. Then type
rungms exam01 >& exam01.log
assuming your input file is called exam01.inp.

There is no graphical user interface for Gamess, but consider Avogadro or Gabedit.


Gaussian and Gaussview

Gaussian is an electronic structure program with a wide variety of Hamiltonians and basis sets. Each Gaussian user is required to sign a license agreement. Email us if you wish to use the software in the MGCF and have not signed a license agreement.

Gaussview is a graphical interface to set up and review Gaussian calculations.

We have both Gaussian16 (uses Gaussview 6) and Gaussian09 (uses Gaussview 5). Start with our tutorials. Even if you have used Gaussian before, our Intro to Gaussian tutorial will take you through the operational steps to run jobs within the MGCF.

Gaussian 16 has online documentation.
A local copy of Gaussian 09 documentation is available from berkeley.edu IP addresses (example eduroam or VPN=yes, Calvisitor=no).

Gaussview should be run on our MGCF workstations but Gaussian calculations should be run on our computing cluster (Tiger). Input files should use a .com extension (not .gjf).

Gaussview can directly submit Gaussian calculations to our computing cluster. The default number of cpu cores is 1 but you can use the Link 0 Tab to request up to 64 cpu cores (we strongly recommend 16 core for most large jobs, 32 core for gigantic jobs, and we have yet to find a job that can really use 64 core efficiently). This puts an %nprocshared entry in your input file which is read by the queue and assigned accordingly. You should assign about 7GB of memory per core. If you ask for more that this ratio you can destabilize other running calculations. Note that the submission software confirms this and will adjust the memory to match the %nprocshared request. On the small nodes (the Cubs), 12 core and 3.5GB per core are the max. If you make com files by hand, make sure there are %nprocshared= and %mem= lines in your file.

When submitting from Gaussview, you see a failed to return a log file error message. Gaussview disconnects from Gaussian when running on the cluster, so you always get that message. Follow your calculation using qstat on the Linux command line. Gaussview can read in the current state of the .out or .chk file while the calculation is still running.

Gaussview 5 will run Gaussian 09 (revision D01). Many people in the MGCF have a Gaussview icon (= Gaussview 5) on your MGCF desktop. If you don't have the icon or are connected remotely, open a Linux command line terminal and type gv5 to start. This will also put the icon on your MGCF desktop for future use.

Gaussview 6 will run Gaussian 16 (revision A03). To start Gaussview 6, open a terminal and type gv6. This will also put a Gaussview 6 icon on your MGCF desktop for future use.

You can also use the command line to directly submit com files to the cluster. For an input file called test001.com you can type:
run_g16 test001
to submit Gaussian 16 revision A03 calculations to the computing cluster.
You can submit Gaussian 09 revision D01 calculations by typing:
run_g09 test001

We also have Gaussian 16 revision B01. To use this, please use the commands run_g16_b01. Once we have tested this somewhat, we will make this the default for run_g16. You will still be able to use Gaussian 16 revision A03 with run_g16_a03 and run_g16_a03.

If you need to run Gaussian (16 or 09) or related utilities (cubegen, formchk) on the local MGCF workstation, open a terminal, type g16_setup or g09_setup. That terminal session will have all system variables set for the chosen Gaussian version.

Right now g16_setup uses Gaussian 16 revision A03. But you can use g16_setup_a03 or g16_setup_b01 to control the revision. We will change g16_setup to point to Gaussian 16 revision B01 once we have finished testing.

We have tutorials and a guide on custom basis sets, convergence issues, restarting, transition state searches, NMR, redundant coordinates, ONIOM, G3, NBO, nice pictures of your output, ESP/Density plots.

We have scripts for creating and submitting multiple jobs from prior chk or xyz files.

Here is a nice guide on solid state calculations.

We also have the anisotropy of the current (induced) density ACID (or AICD) program.

See the Gaussian site for more information.

Cubegen error: Gaussview5 is not always able to read Gaussian09 C01 or D01 chk files for cubegen. Please see our workaround for rev C01 and rev D01.

If you have many G16 cube files to generate, you can use run_cubegen to run on Tiger.

If you connect remotely from Mac/Windows and have GaussView display bugs, type mesagl immediately before starting GaussView. This will set the USE_MESAGL environment variable.


GaussSum

This is a utility program to extract information from Gaussian output. Most users will use Gaussview (below) but there are some applications for which GaussSum might be helpful. This is available on the MGCF workstations in 175 Tan Hall (not Tiger). See the home page for usage information. Type gausssum to start.


GIMP

is the GNU Image Manipulation Program. It has many features found in Photoshop. This is on the MGCF workstations in 175 Tan Hall (not Tiger). Type gimp to start. See the GIMP home page for documentation.


gnuplot

This is a command driven interactive plotting function available on the MGCF workstations. Type gnuplot to start. Type man gnuplot or see the FAQS for more information. This is a nice program but see the listing for Scilab.


gOpenMol

This is old software but we keep it available in case it proves useful. It can visualize chemical properties, total electron densities and molecular orbitals using data from Jaguar, Gaussian, Gamess, etc.

It comes from the Finish IT center for Science. Tutorials and lots of usage information is here. We have a manual and basic user guide in /usr/software/gopenmol on the MGCF workstations (not Tiger). Type gopenmol to start.


Gromacs

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids but many groups are also using it for research on non-biological systems, e.g. polymers.

See the Gromacs home page and documentation. See tutorials here. Many others are available but be sure to check they refer to recent gromacs versions. There were major changes from version 4 to 5 and input files are NOT interchangeable. Online documentation can be confusing since it may not be clear which version is being used. The MGCF is using the 5 series, version 2018-4 (workstations) and 2019-3 (tiger).

Type gromacs_setup to enable the software for a single terminal session. Note, as you read online docs, you may see instructions to source XXX/bin/GMXRC. This is not needed since it is built into the gromacs_setup command.

Gromacs autodetects gpu cards and will use them. On bambam and barney, be sure to use -gpu_id 1 in your mdrun command since there are 2 gpus labelled 0 and 1. Card 1 is much faster. On other MGCF workstations, the autodetect should be fine.

On tiger, we are working on making a run_gromacs script. Let us know if you are waiting on this.


GSAS

GSAS (General Structure Analysis System) is a comprehensive system for the refinement of structural models for x-ray and neutron diffraction data. It can be used with single-crystal and powder diffraction data (Rietveld analysis).

This is available on the MGCF workstations (not Tiger). The manual is in the /usr/software/gsas folder. Type gsasgui to start.

GSAS can be obtained from the NIST Center for Neutron Research.

Another useful site is the SINCRIS Information Server for Crystallography.

Data conversion software for gsas input can be found at the ccp14 site.

We also have NCNR Ciftools which includes pdCIFplot, used to plot of Rietveld results from pdCIF files, particularly for referee review and cifedit, used to create and edit CIF files. It may be used with all types of CIF files, including mmCIFs.


Gulp

GULP performs simulations on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). It uses analytical solutions with lattice dynamics, rather than molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons.

To load the environment variables on the workstations, type:
intel
source /home/mgcf/software-ws/gulp-5.2/MGCF_setup-mpi-run.sh
These should be typed once per terminal when you plan to use gulp.

For a multicore job, type:
mpirun -np 2 gulp < example1.gin > example1.gout
For a one core job, type:
gulp example1
Note the lack of file extension or redirect to an output file for the 1 core job.
This 1 core vs multicore syntax is different from what the manual says! The input file is example1.gin in both 1 core and multicore cases, but you only type the example1 prefix in the command to run the 1 core job. In the multicore job, you type the whole file name.

Documentation and example files are in
/home/mgcf/software-ws/gulp-5.2
For more information, see the home page.

If you need more Gulp libraries or a run_gulp command to run on Tiger, let us know.


HEX

Hex is older program for protein-protein or protein-DNA docking.
Maestro and its related programs are more current for this kind of calculation but we keep Hex in case it is useful for someone.
Hex is on the MGCF workstations (not Tiger) and has built in documentation and tutorials. Type hex to start.
For more information, see the home page and our Hex HowTo.


Hoomd-blue

HOOMD-blue is a general-purpose particle simulation toolkit optimized for execution on both GPUs and CPUs. You can get tutorials with:
git clone https://github.com/glotzerlab/hoomd-examples.git
cd hoomd-examples
Note note we observe that line 13 of ex_render.py should be:
preview_tracer = fresnel.tracer.Preview(device, 300, 300, 3)


To start, type:
anaconda3_setup
conda activate hoomd-blue
jupyter notebook
For more information, see the home page. Right now this is on the MGCF workstations (not the cluster, Tiger).


Igor Pro

is an interactive software environment for experimentation with scientific and engineering data and for the production of publication-quality graphs and page layouts.

This is Windows/Mac only and since the MGCF workstations are Linux based, see our Windows page for access and use information.

Kavli/MGCF users can request access to use this on their own Windows or Mac machines by filling out this form (requires berkeley.edu authentication).

See the home page for more about Igor Pro.


ImageJ

is a public domain Java image processing and analysis program to display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and raw. It supports stacks and hyperstacks, a series of images that share a single window.

It can calculate area and pixel value statistics, measure distances and angles, create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

It is installed on the MGCF workstations. Type imagej to start the interactive program. There is suite of command line tools as well.


ImageMagick

is a software suite to create, edit, and compose images. It can read, convert and write images in over 100 formats including GIF, JPEG, PDF, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bezier curves.

To edit an image file, type display filename and click anywhere in the image window to bring up the control panel. There is suite of command line tools as well.

This software is installed on the MGCF workstations.


IQmol

is a free open-source molecular editor and visualization package including surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways). It offers an intuitive enviroment to set up, run, and analyse Q-Chem calculations but it can also read and display a variety of file formats, including formatted checkpoint files.

It is on all MGCF workstations in 175 Tan Hall, not on Tiger.

Type iqmol to start the program.

For more information, see the home page and manual.

Please note, while IQmol works as a builder for Q-Chem, it does not submit to the queue on Tiger. Write a input file from IQmol and then use run_qchem.

Unfortunately IQmol does not work over X2Go. We recommend you download your own copy (it is free and works on Mac/Windows). Then transfer files as needed.


Isostar

is a library of nonbonded interactions formed by a wide variety of chemical groups. It brings together data on nonbonded interactions from three sources: the Cambridge Structural Database (CSD) of small-molecule organic and metallo-organic crystal structures, the Protein Data Bank (PDB), and ab-initio based molecular orbital calculations. One can select a functional group and investigate its nonbonded interactions with a second group. A 3D scatterplot shows the experimental distribution of the interactions between the groups as observed in crystal structures taken from the CSD or PDB.

To get started, open a web browser on any of the linux workstation in our lab. Then click this isostar link.
Make your selections and download the filename.istr when prompted. Then open a terminal, cd to the folder where the istr file was downloaded, and type:
run_isostar filename.istr
When the new Isostar application opens, click the Hyperlink box.

If you have trouble at this step, ask us for help. Firefox does not recognize the istr file type. If you are using Isostar a lot, we can help you add this to the firefox handlers.json file so it opens automatically.


Jaguar

is fast ab initio electronic structure software. Pseudospectral methods to calculate two- electron integrals and correlation techniques that are local allows the HF, DFT, MP2, GVB, and GVB-RCI methods to scale better than N3 (where N is the basis set size).

Jaguar is distributed by Schrodinger and the graphical interface is Maestro. Type maestro to start the graphics interface (only do this on the linux workstations, not on the server). See the documentation and tutorials.

As you set up the calculation, use the Gear pulldown from the Job panel and choose tiger_jaguar as the host. Do not increase the number of Threads. Ask for advice before increasing the number of cpus. Click Run. If you don't specify the host, your calculation will run on the workstation where you are using Maestro. This is okay for short jobs but be aware that Jaguar jobs often take many hours. Once the job is submitted, close Maestro, logout and come back to review later on or the next day.

qstat
will show you the status of your job on the server. Only 10 jaguar jobs can be run simultaneously due to a license restriction. If you submit > 10 jobs, the extra will be queued to wait for a free license. Jaguar job names show up in qstat as j-jobname.

If you are running on the workstations, topw will show you the top processes on each machine.

For ESP or Density Plots, see the Documentation and the Schrodinger knowledge base on Jaguar ESP. You can control the range of ESP values to be mapped. If you want to compare multiple structures, use the same the minimum and maximum values for each. The units of the ESP are kcal/mol.


Jalview

is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

See the home page. This software is installed on the MGCF workstations (not Tiger). Type jalview to start the program.


Jmol

is a java based, free, open source molecule viewer. It supports RasMol/Chime scripting, displays inter-atomic distances, bond angles, and dihedral angles, vectors (velocity, dipole, etc.), charges, and atomic symbols, unit cell boxes, and energy bands, animates the results of simulations and computed vibrational modes, reads many types of files: ABINIT, ACES II, ADF, CIF/mmCIF, CML 1/2, Dalton, GAMESS, Gaussian, Ghemical, HIN, Jaguar, MDL molfiles, MOPAC, PDB, VASP, XYZ (XMol), prints or exports images in these formats: GIF, JPG, PPM, BMP, PNG, PDF, PostScript, and PovRay (including animations).

It is installed on the MGCF workstations (not the server). Type jmol to start the program.


Knime

(Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. It has integrated workflows from the Schrodinger software, plus the Chemistry Development Kit, the R Statistical Computing package, and the Weka Data Mining package.

See the home page. This software is installed on the MGCF workstations (not Tiger). Type knime to start the program.


LAMMPS

(Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code. It has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically as a parallel particle simulator at the atomic, meso, or continuum scale.

It is available on all of the linux workstations in 175 Tan Hall and on on Tiger.

On the workstations, type lammps_setup before you start to load the right environment settings. The executable name is lmps and it is mpi enabled.

To submit Lammps jobs to Tiger, login in to any MGCF workstation, then cd to the calculation folder (one calulation per folder is advised). Then type:
run_lammps input_file num_core
example:
run_lammps in.Zn2dopbd 8
This will create a new file: input_file.job. Inspect that file for errors. Then type
qsub input_file.job

Use qstat to follow it or qdel to delete it. Up to 64 core should be fine. More might be possible but we have not tested it. Let us know if you want help with this.

For more information, see the home page. There are lots of third party tools for input and analysis.

We have the lammps-interface tool installed. Type
anaconda3_setup
(required once per terminal session, do not put this in your .bashrc) and then type
lammps-interface filename.cif
This will create 2 files: data.filename and in.filename
You may see: fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
but this error can be ignored.

We have TopoTools in our version of VMD. There are sample inputs and tutorials at that page.


Lumerical FDTD

High performance 3D FDTD-method (Finite-Difference Time-Domain) Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. 3D CAD environment and parameterizable simulation objects, multi-coefficient models for accurate material modeling over large wavelength ranges, non-linear materials and spatially variable anisotropy, powerful post-processing capability, including far-field projections, band structure analysis, BSDF generation, Q-factor analysis and charge generation rate, extensive geometry import options, and scripting. The advanced conformal mesh gives high accuracy, even with coarse meshes. Bend loss, confinement factor, and modal area analysis. Simulate large planar waveguides with the accuracy of 3D. Simulate optical components using optical, electrical, and thermal multiphysics.

It is on all of the MGCF and Kavli linux workstations in 175 Tan Hall, not on Tiger. We have a very limited number of licenses. Close the program when not in use.

Type fdtd to start the program.

For more information, see the home page.


MacroModel (also see Maestro)

This program was developed by W. Clark Still at Columbia University and is distributed by Schrodinger. It performs molecular mechanics minimizations, conformational searches, molecular dynamics, etc. on organic and bioorganic molecules using a variety of force fields including MM3, Amber and OPLS.

The graphical interface for this program is Maestro (next section). See the documentation.


Maestro

(version 2021-2 as of June 1, 2021) is a graphical interface for a suite of biomolecular and chemistry programs from Schrodinger Inc. Key programs are:
Macromodel for minimizations and conformational searches on organic and bioorganic molecules using MM3, Amber and OPLS force fields.
Glide for ligand-protein docking.
Piper for protein-protein docking.
Jaguar for DFT.
Desmond for molecular dynamics.

We have tutorials. See also the Maestro Quick Reference Card, the documentation, videos.

Maestro runs on our MGCF workstations but compute jobs (Macromodel, Jaguar, Desmond, etc) can be run on the server.

Type maestro to start the latest version.
Type maestro202 to start the prior version.

If Maestro crashes and locks up, open a terminal and type
killall maestro
on the command line.


Materials Studio

is a client/server package with various computational chemistry modules, with a particular focus on applications in materials research. The client software is Windows only (there is no Mac or Linux client but it is quite easy to set up and run it on a virtual machine). Each time you start the program, a license must be checked out from our server.

This is Windows only and since the MGCF workstations are Linux based, see our Windows page for access and use information.

Please email us to request access. You should email us from a berkeley.edu address, and explain your status as a CoC/Kavli or other MGCF user.

Materials Studio has many Modules. We also have the academic versions of many of these modules including Castep and Gulp. It is better to use the academic versions when available in order to maintain the limited number MS licenses.
More information is available from 3DS (formerly Biovia, Accelrys, MSI).

Materials Studio documentation is available from berkeley.edu IP addresses (example eduroam or VPN=yes, Calvisitor=no).

A very nice tutorial was written by Chris Trickett in the Yahgi group. A version modified for the MGCF is maintained here.


Mathematica

is a programming environment for mathematical manipulations and plotting including numeric and symbolic computations, interactive document capabilities, an advanced programming language, graphics, polynomials, integrals, etc.

If you have never used Mathematica in the MGCF, type Mathematica_license_setup before you start the first time. This adds license credentials to your home folder. You only need to do this once in the duration of your MGCF login.

To reduce conflict with Matlab which has similar executable names, you must type Mathematica_setup before you start each terminal session. This loads Mathematica executables into the PATH for the remainder of the current terminal session.

Then type mathematica to start the main program.

If you use it on the cluster in a script, add /home/mgcf/software-ws/Wolfram/Mathematica/bin to your PATH. Ask for help if this is unclear.

Documentation, sample programs, etc are available.


Matlab

is a math programming language, combining tools for numeric and symbolic computation, graphics and visualization, simulation, algorithm prototyping and application development. It offers support for multidimensional arrays and user-definable data structures.

Matlab R2020a is the default. If you need older versions, you can add /home/mgcf/software-ws/MATLAB/R201XX/bin to the front of the PATH, where XX is 9a, 9b, etc. Email MGCF staff for help. Versions older than 2 years will eventually be deleted so let the staff know if you need these.

Most interactive work or calculations of less than 24 hours should be run on the MGCF workstations. To use Matlab on the cluster, make a script and submit it to the queue. Here is a sample script and sample input. To run the example, download the two files to your home directory and then:
qsub matlab.job You can also type
run_matlab example.m num_core
to make an example.job file.
Follow your calculation using qstat. You can delete a running calculation using qdel job_id where job_id is the number in the first column of output from qstat.

On the MGCF workstations, type matlab to start the Matlab graphical interface.

Documentation, tutorials and examples are at http://www.mathworks.com/access/helpdesk/help/techdoc/matlab.shtml

Technical support is available directly from tech@mathworks.com

See also the Matlab home page.


Mercury

is for visualising crystal structures in 3D including H-bonding and other short contacts, build and visualise a network of contacts, packing diagrams of single and multiple cell contents, measurement of geometrical parameters, centroids, least-squares mean planes and Miller planes, ability to display slices through a crystal in any direction.
For more information, see the CCDC.

This is on all of the linux workstations (not Tiger).
Type mercury to start the program.

If you use this software remotely (via X2Go), different graphics libraries are required. This should happen automatically, but if the program crashes when starting, type gl_preload and then type mercury again.

If you encounter a license error, type csd_renew. Please let us know if these problems persist.

We have an occasional problem where Mercury cannot browse to open files. The problem is related to a misconfigured file in the /home/username/.config folder. The fix is to open a terminal and type:
rm ~/.config/Trolltech.conf
Then close/open mercury.
Note it is .config, not config. File and folder names beginning with . are hidden. Also ~ is a linux variable meaning /home/username.

We also have the related CCDC utilities: encifer and rpluto (probably legacy software).


MMTSB Tool Set

Multiscale Modeling Tools for Structural Biology. These are tools for dealing with biomolecular structures and related computational data.

See the home page for command documentation.

This is available on the linux workstations but is not automatically loaded in your login. You will have to type "mmtsb" once per shell session. That will load the MMTSB tools into the shell session and disable similarily named software.


MNova

NMR Data processing software from Mestrelab. We have a site license maintained by the NMR facility. You must be on a UC Berkeley authenticated network like eduroam or VPN to reach this content.

You can obtain the software from the NMR Facility but we are migrating that content here where it might be a little easier to access. This requires a UC Berkeley bmail sign in.


Modeller 9v5

is used for homology modeling of protein 3D structures. Provide an alignment of a sequence to be modeled with known related structures and MODELLER calculates a model. MODELLER can perform de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. See the home page for tutorials and faqs.

This program is available on the linux workstations.


MOLDEN

We are running version 5.9.6 as of April 2019. This program has a very long history and the interface is a little quirky. It is a visualization tool for displaying output from GAMESS, GAUSSIAN, Mopac and many other computational chemistry programs. It can display MO's, electron density, and Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden is also capable of importing and displaying of a variety of molecular structure files.

In the MGCF, we find it has been very useful in converting old file formats including ancient MSI files. The Molden home page is a good source of information on this program. It is available on the MGCF workstations. Type molden to start the program. There is a GL version called gmolden. If you use this remotely (via X2Go), different graphics libraries are required. This should happen automatically, but if the program crashes when starting, type gl_preload and then type molden or gmolden again.


Molekel

is an older 3D molecular graphics package. It can calculate isosurfaces of electron and spin densities as well as MO's from various electronic structure calculation output. It has texture mapping to color code surfaces, can clip any surface by a clipping plane and render it transparent. It can animate and display vibrational modes and can animate geometry optimizations, trajectory files and multiple coordinate PDB files. Supported output file formats of electronic structure calculation programs: Gaussian, Gamess, ADF, Zindo, and others.

Molekel is vailable on our MGCF workstations (not Tiger). Type molekel to start the program.

See the home page for information and documentation.


MolGW

MOLGW implements the many-body perturbation theory (MBPT) to describe the excited electronic states in finite systems (atoms, molecules, clusters). It most importantly implements the GW approximation for the self-energy and the Bethe-Salpeter equation for the optical excitations.

MolGW should be run on Tiger but if you want to do input testing, you can do short runs on the MGCF workstations. To run on MGCF workstation command line, type
molgw_setup
to set environment variables for that session.
Then type:
molgw example.in
replacing example.in with your input file name. If it dies, then use the screen output to debug your input. If it runs okay for a few minutes, then type Ctrl-C to kill the interactive run. You can then use run_molgw to submit to Tiger.

Each MolGW job should be run from its own folder. Make a folder for the calculation and move the input files to that folder.

On the command line, type
cd foldername
where foldername is the folder name with input files.
To start jobs on Tiger:
run_molgw jobname <number_of_core>
to start your job in the queue on Tiger.

See the home page for documentation and examples.


MOPAC

(Molecular Orbital PACkage) is a general-purpose semiempirical molecular orbital package. MOPAC2016 is the latest version. The semiempirical Hamiltonians MNDO, AM1, PM3, PM6, RM1, MNDO-d, and PM7 are used in the electronic part of the calculation. One can get molecular orbitals, heat of formation, vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants. Transition state location and optimization are available. PM6 and PM7 can calulate polymers such as bucky tubes (1D), surfaces (2D), and crystals (3D) with periodic boundary conditions. This is on the MGCF workstations (not Tiger).

See the current manual. Mopac has been used in Lanthanide Complexes.

There is no GUI but the Lanthanide Complex page has a nice discussion about how to use Gabedit to set up inputs. Also, babel can convert mol2 files to Mopac input format. Then keywords can be added manually using a text editor.

Type the following to run the program:
mopac inputfile
Most runs are so quick that they will be done in seconds but for longer jobs that need to survive after logout, use:
nohup mopac inputfile &


MPB 1.7.0

The MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. It was developed by Steven G. Johnson at MIT along with the Joannopoulos Ab Initio Physics group. This program computes definite-frequency eigenstates (harmonic modes) of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors, using fully-vectorial and three-dimensional methods. It is especially designed for the study of photonic crystals (a.k.a. photonic band-gap materials), but is also applicable to many other problems in optics, such as waveguides and resonator systems. (For example, it can solve for the modes of waveguides with arbitrary cross-sections.)

Type mpb_setup just before you run the program. This sets the correct environment variables to run the software from the current shell.
This is only on the MGCF workstations, not Tiger.

The manual is available.

See the MPB site for current links and more information.


Multiwfn

is a free, open-source, powerful wavefunction analysis program, supporting many wavefunction analysis methods. Multiwfn accepts several kinds of files for inputting wavefunction information: .wfn/.wfx (Conventional / Extended PROAIM wavefunction file), .molden (Molden input file), .31~.40 (NBO plot file), .fch (Gaussian formatted check file). Other file types such as Gaussian .cub file, DMol3 .grd file, .pdb, .xyz file and plain text file are acceptable for specific functions.

See the home page for details. In the MGCF, type multiwfn to start the program. This is on the workstations, not Tiger. There is a manual and a Quick Start Guide.


NAMD

is a parallel molecular dynamics program designed for high-performance simulation of large biomolecular systems. NAMD has been developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. The home page has documentation and tutorials. To use this on the workstations, first type namd_setup for the multicore version or namd_setup_gpu for the gpu versrion. This sets the correct environment variables to run the software from the current shell.
To start jobs on Tiger:
run_namd jobname <number_of_core>
run_namd_gpu jobname <number_of_threads>


NBOView

NBOView is a program for viewing the natural bond orbitals from an NBO calculation. It can generate 1D and 2D plots as well as high-quality 3D images of any of the orbital types available in NBO. The program is started by typing nboview on the command line from the directory containing your input files.

NBOView requires files generated by including the PLOT keyword in the NBO input. For more information, please see the home page.

Important: Depending on the electronic structure program from which the NBO analysis was run, specific procedures are necessary to generate the plotting files. See our instructions on how to do this for Gaussian.


NCIPLOT

is a program for viewing NCI (Non-Covalent Interactions) based on the peaks that appear in the reduced density gradient (RDG) at low densities. There is a crucial change in the RDG at the critical points in between molecules due to the annihilation of the density gradient at these points. NCIPLOT computes density and reduced density gradient (RDG) on a grid and provides Gaussian-format cube files and VMD scripts for the direct visualization of the results. It can be run using either SCF densities (wfn input files) or promolecular densities (xyz input files), which makes it applicable to large biosystems.

For more information, please visit the home page. documentation and example files are in /usr/software/nciplot on any facility workstation. Type nciplot to run the program, but you must read the documentation first since the program requires command line inputs.


NWChem

is a quantum mechanical program for molecular and periodic systems. It can also perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed QM/MM simulations. It is developed at the Pacific Northwest National Laboratory (PNNL).

We are using NWChem version 7.0.0 as of December 1, 2019.
You can run a single core NWChem job with the command:

run_nwchem jobname.nw

Type run_nwchem on any MGCF machine and you will see the options.
For multi core jobs, the command is:

run_nwchem jobname.nw number_of_core

NWChem may generate files with nonunique names. You should run individual NWChem jobs from separate directories.

run_nwchem puts scratch files in /scr on each compute node, then deletes them at the end. Let us know if this strategy needs modification.

See the documentation and homepage for details.

Avogadro is a good choice as a GUI. We also find that JMol is a good utility for reviewing NWChem output files. NWChem is available on Tiger. Avogadro and JMol are on the workstations.


Optados

is code for calculating optical, core-level excitation spectra and electronic density of states (DOS). OptaDOS uses CASTEP output files, although it is extendible to perform calculations on output by any electronic structure code.

To run on Tiger, type
cd foldername
where foldername is the location of the castep output data and an optados input file with an .odi extension.
run_optados filename.odi
for a 1 core job
or
run_optados example.odi 4
for a 4 core job.

We have a example files on the MGCF workstations in /home/mgcf/software-ws/optados/optados/examples
See the home page for the manual and examples.



Orca

is a quantum chemistry program with emphasis on spectroscopic properties (including EPR) of open-shell molecules. It includes Semiempirical (INDO/S, MNDO, AM1, PM3, NDDO/1), Hartee Fock (RHF, UHF, ROHF and CASSCF), DFT (exchange and correlation functionals, hybrid DFT, double hybrid functionals), single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local), multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI), TD-DFT and CI-singles (CIS). It also has ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches. The COSMO model is available for continuum dielectric modeling.

To run a test job on the MGCF workstations in 175 Tan Hall, open a terminal, type
orca42_setup
or
orca5_setup
That terminal session will have all system variables set for Orca version 4.2 or 5.

To run on Tiger, type
run_orca42 filename.inp
or
run_orca5 filename.inp

We have a sample input file.

Note that nprocs is set in the inp file and not in the run_orca5 or run_orca42 command.

We have an Orca Notes Document. This covers important differences in version 5 vs 4.2 and also how to manage memory intensive jobs such as DLPNO-CCSD(T) calculations on large molecules.

See also the Orca Forum and the Orca Input Library for more information. MGCF ORCA Excited State tutorial.


Origin Pro

Origin does data analysis and publication-quality graphing. It has extended analysis tools in the following areas: Peak Fitting, Surface Fitting, Statistics, Signal Processing, Gadgets, Image Processing.

This is Windows only and since the MGCF workstations are Linux based, see our Windows page for access and use information.

The Origin home page is a good place for more information.


PaDel-Descriptor

PaDel-Descriptor calculates 1875 molecular descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints (total 16092 bits). This can be useful data for machine learning.

This software is on the MGCF workstations (not Tiger).
Type padel to start the program.

The journal reference and home page have more information.


Phenix

Python-based Hierarchical ENvironment for Integrated Xtallography
is on the MGCF workstations (not Tiger).
Type phenix to start the program. If you want to use the other utilities associated with phenix, type: phenix_setup to activate this suite for that shell only.

The Phenix page has documentation and references.


Platon

is a versatile, SHELX97 compatible, multipurpose crystallographic tool. See the home page

This software is on the MGCF workstations (not Tiger).
Type platon to start the program.


PYMOL

is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.

This software is available on our MGCF (not Tiger) machines.
Type pymol to start.

Pymol is a little buggy over X2Go. When you type pymol, it will run a script to detect if you are on a remote connection, or if you are seated in the MGCF computer lab. For a remote connection, the script sets an environment variable:
LD_PRELOAD=/home/mgcf/libs/libGL.so.1
which is an older version of libGL that is more stable on X2Go.
Next, the script checks your home folder for a .pymolrc file. If you don't have one, the mgcf version will be copied your folder with the built in setting:
set use_shaders, 0
If you make your own .pymolrc file, then you must include a set use_shaders, 0 line. But otherwise, you don't have to do anything. We are mainly posting this so other people searching for this solution can find it. Without the .pymolrc setting, the program will crash when opening a pdb file.

More information can be obtained at The PYMOL home page and also Practical_Pymol_for_Beginners.


Python

The MGCF workstations have Python 2.7 and 3.6 embedded in the operating system (Centos 7). Anaconda and pip are part of Centos 7 but are of limited use for non-root users. We have built a separate Anaconda installation for users. Type
anaconda2_setup (for Python 2.7)
or
anaconda3_setup (for Python 3.7)

We have preconfigured environments (most in anaconda3) which you can activate:
conda activate tensorflow
conda activate compilers
(for mpi4py and related tools, note these tools are in many other of these environments)
conda activate matsci
conda activate biopython
conda activate rosetta (for PyRosetta, use anaconda3_setup).
conda activate hoomd-blue (use anaconda3_setup; see tutorials)
conda activate molmod https://molmod.github.io/molmod/
conda activate keras Deep Learning
conda activate AID_framework Machine Learning for transition state searching.

We recently added an new option:
anaconda38_setup (for Python 3.8)
and these environments:
conda activate morfeus calculates molecular features and steric descriptors from 3D structures.
conda activate pyscf Python-based Simulations of Chemistry Framework.

Let us know if you need packages or environments added or updated. You can install your own Anaconda environments in your home folder but we are happy to add commonly used environments to our Anaconda. Email us with what you need and we'll try to help.

For a Jupyter notebook, you could type anaconda3_setup and then jupyter notebook in a terminal window.
These environments are on our MGCF workstations in 175 Tan Hall.
To use anaconda environments on the cluster (Tiger), type run_anaconda [num_core] to make a job file and then edit the job file for your needs. [num_core] should be 1 unless your code runs in parallel. Type run_anaconda without a number to see options. Please ask us for help! The num_core used by your code must match the queue allocation and this requires care to get right.


Q-Chem

is an efficient quantum chemistry program including Hartree-Fock, DFT with accurate linear scaling algorithms and efficient post-HF correlation methods. Calculations can be extended with QM/MM and molecular dynamics. See the home page and the version 5.4 manual or version 5.3 manual for details.

The recommended graphical user interface is IQmol. This is on the MGCF workstations in 175 Tan Hall.

See the Official Q-Chem/IQmol Tutorials.
We also have MGCF QChem tutorials and a QChem Tips page for some advanced calculation types and discussion about versions.
Also look in the folder /home/mgcf/software-ws/qchem/samples for examples.

From the MGCF workstations, to run a single core job on Tiger, type:
run_qchem jobname
or
run_qchem54 jobname
or
run_qchem541 jobname
where jobname is the input file named jobname.in or jobname.inp in the current folder. This starts a 1 core calculation with Q-Chem.
run_qchem54 is version 5.4.0 and run_qchem541 is version 5.4.1.
run_qchem = run_qchem541 as of August 19, 2021.

Email MGCF staff if you need older versions so we continue to maintain them. The licenses are quite short term so we delete old versions after about a year.

You can request up to 64 core using
run_qchem jobname num_core
where num_core is the desired number of core for the job. You can request up to 64 core in shared memory although few jobs can really use 64 core efficiently. We strongly recommend 16 core for most large jobs, 32 core for gigantic jobs. You can use up to 7GB RAM per core.
Ask for help until you get the hang of this.

Follow your calculation by typing qstat on the Linux command line.

Please see also issues related to running Q-Chem in parallel.
run_qchem
without flags will provide information about options.
We recommend doing opt+freq calculations in shared memory (same as OpenMP, this is the default setting) rather than via MPI. Other algorithms require different settings. The syntax of these options are built into run_qchem provided you choose the default or MPI at submission.

If you need to run Q-Chem on a local MGCF workstation (for very short jobs or input testing only!), open a terminal, type qchem_setup or qchem_setup_mpi. This sets the current Q-Chem enviroment variables in that termial, in shared memory or MPI mode. To control versions, use qchem541_setup or qchem541_mpi_setup for version 5.4.1 and qchem54_setup or qchem54_mpi_setup for version 5.4.0. For MPI in this type of use, you must use the Q-Chem in parallel syntax unlike the run_qchem process which has it built in.


Qikprop

is a quick, accurate, easy-to-use absorption, distribution, metabolism, and excretion (ADME) prediction program. It predicts physically significant descriptors and pharmaceutically relevant properties of organic molecules. QikProp provides ranges for comparing molecular properties with 95% of known drugs. It flags types of reactive functional groups that may cause false positives in high-throughput screening (HTS) assays.

This is available on the MGCF workstations. The graphical interface for Qikprop is Maestro. Type maestro to start the graphical interface.
See also the current documentation and the Schrodinger site.


Quantum Espresso

(version 6.6 as of June 2021) does DFT based electronic-structure calculations including plane waves and pseudopotentials. See the home page and faqs for details and tutorials.

QE can be run through Maestro or as a stand alone program.

There is also a Materials interface. Please request that we put this icon on your MGCF desktop.

Materials is a GUI to all of the same underlying software as Maestro, but in Materials, the menus are more focussed on Materials related tasks rather than organic/bioorganic.

To run stand alone, if you have a input called exam01.in type:
run_espresso exam01
You can request up to 64 core using
run_espresso exam01 num_core
where num_core is the desired number of core for the job. This will run on our server, Tiger.

Follow your calculation using qstat on the Linux command line. See the faq on queue commands.

PWgui can help configure input keywords but much of the configuration will be manual. Type pwgui to start it.

Examples, test inputs and documentation are in
/home/mgcf/software-ws/quantum-espresso-examples
Recommended pseudopotentials are in /home/mgcf/software-ws/q-e_schrodinger-pseudo
You don't need to copy them. Just specify
pseudo_dir = '/home/mgcf/software-ws/q-e_schrodinger-pseudo' ,
in the &CONTROL section of your input.
Note that with QE version 6.6 (June 2021), major changes were made to the pseudopotentials. The recommended folder has the new versions.

pseudo_dir = '/home/mgcf/software-ws/q-e_schrodinger-pseudo.old' ,
contains the older format pseudopotentials.

Let us know if you need other pseudopotentials or want to continue using the older QE (version 6.4).

Write temporary files to /scr. Do not use the variable "outdir" in your input file. This creates too much I/O on the server. The name of the outdir will instead be set in the run_espresso script using an environment variable called ESPRESSO_TMPDIR, which is created at runtime to be /scr/$USER/$JOB_ID so it is both unique and in the local scratch folder on the node. The output is copied to the home directory at the end of the job.

See the home page and faqs for input descriptions and more details about QE.

To do a quick test of your inputs on a MGCF workstation, first type
qe_setup
This will set appropriate environment variables in the current window only (for QE version 6.6).
Then type:
pw.x < example.in
replacing example.in with your input file name. If it dies, then use the screen output to debug your input. If it runs okay for a few minutes, then type Ctrl-C to kill the interactive run. You can then use run_espresso to submit to Tiger. However it is fine to run very small jobs in the background on the workstations. The syntax is:
nohup pw.x < example.in > example.out &
or for multi core (example uses 4 core)
nohup $ESPRESSO_ROOT/run_qe pw.x 4 local.in > local.out &
If you are running on the workstations, topw will show you the top processes on each machine. top shows the current machine's processes. kill -9 PID can be used to kill the process. PID is the process id number shown by top.


R

is an integrated suite of software facilities for data manipulation, calculation and graphical display. It provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which publication-quality plots can be produced, including mathematical symbols and formulae. It has a simple and effective programming language which includes conditionals, loops, user-defined recursive functions and input and output facilities.

For more information, see the R Information page.


R/Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data using the R statistical programming language. It has over 700 programs (not all of which are installed, but any can be installed if you email us. These include tools for annotation, array assay, bioinformatics, mass spectrometry, and sets of experimantal data.

For more information, see the Bioconductor home page.


RCSB-LigandExplorer

visualizes Protein Data Bank (PDB) data such as the interactions of bound ligands in protein and nucleic acids structures.
This is available on the linux workstations (not Tiger). It should auto load in your browser if viewing the PDB site. If not, type ligand_explorer to start the program.


Rosetta Commons

Rosetta Commons is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. This is a powerful program but with a steep learning curve. More information is at home page. The Getting Started sequence is really helpful. The program and demo files are installed on MCGF workstations in the /home/mgcf/software-ws/rosetta folder.

Type rosetta_setup to configure the environment variables needed for Rosetta. These settings are only active for that one terminal session. We have MGCF Rosetta Notes about how to run Rosetta on the workstations and Tiger.

PyRosetta is also installed as a Python site-package. See our Python section.

For free online use of some of these tools, try Robetta Server.


Scilab

is a free scientific software package for numerical computations in engineering and scientific applications. It includes hundreds of mathematical functions with the a program interface (C, Fortran...). It has sophisticated data structures (including lists, polynomials, rational functions, linear systems...), an interpreter and a high level programming language. Scilab is an open system where users can define new data types and operations.

This is on the MGCF workstations (not Tiger). Type scilab to get started.
More information and documentation is available at the Scilab home page.


Solidworks Professional Research

is a 3D CAD program where you can create fully detailed parts, assemblies, production-level drawings, generate complex surfaces, sheet metal flat patterns, and structural welded assemblies. It includes wizards to automate designs, perform stress analysis, etc. Solidworks Professional includes libraries of standard parts and fasteners, tools to estimate manufacturing costs and help convert imported geometry, and utilities that search designs for errors.

This is Windows only. Most MGCF workstations are Linux based so see our Windows page for access and use information.

The Solidworks home page is a good place for more information.


Spartan

is a multifaceted tool, allowing for computation and visualization of organic, organo-metallic, and bio-organic molecules using ab initio, dft, semi empirical, and molecular mechanics methods.

Spartan is available on the MGCF workstations (not Tiger).
We only have 3 license tokens so please quit the program when not in use. When you start the program, you checkout a license token. The token is released when you quit. If 3 copies of the program are running, then a 4th copy will not start until one of the others is quit.

Type spartan to start the program.

If you use this software remotely (via X2Go), different graphics libraries are required. This should happen automatically, but if the program crashes when starting, type gl_preload and then type spartan again.

See also the Spartan home page and manual.


Sterimol

A command line Python program for the calculation of multi-dimensional Sterimol parameters: L, B1 and B5 for half-sandwich complexes and organic molecules. If used on half-sandwich complexes, it also generates Tolman cone angles and metal to ring-centroid (unweighted) distances. Code developed in the Paton group at Colorado State University.

It can use Gaussian files as input. It is installed on the MGCF workstations (not on the Tiger cluster). Usage instructions are at the github page but there are small changes.

To use the program on the MGCF workstations, type
sterimol_setup
to set the right environment variables for that shell.
Next, use the full path to call the program:
python /usr/software/Sterimol/sterimol.py gaussian.out

Links: Github page and reference.



Tinker

is a package for molecular mechanics and dynamics, with special features for biopolymers devleped by the Ponder group at Washington University (St. Louis). It can use Amber, CHARMM, MM2 and MM3, OPLS, MMFF, Liam Dang's polarizable potentials, and the Ponder group's own AMOEBA polarizable atomic multipole force field.

To use the tinker subprograms on the MGCF workstations, type tinker_setup first to set the right environment variables for that shell. See also the folders /home/mgcf/software-ws/tinker/examples and /home/mgcf/software-ws/tinker/params.

Links: home page, manual, tutorial from UCSB

There is a GUI called Force Field Explorer.
Email us if you want us to put an icon on your Desktop.


Tonto

is a tool for quantum crystallography and quantum chemistry. It can do wavefunction fitting in which Hartree Fock/DFT calculations are constrained by some experimental data, typically from X-ray diffraction studies. It can refine crystal structures using ab initio wavefunctions. It can also fit electronic wavefunctions to X-ray diffraction data.

See also the folders:
/home/mgcf/software-ws/tonto/tests
/home/mgcf/software-ws/tonto/basis_sets

Links: home page, wiki page, How-to-run page, theory, more theory


Vasp 5.4.4

is the Vienna Ab initio Simulation Package for electronic structure calculations on materials including quantum-mechanical molecular dynamics. It is currently licensed only for the Bell and Iglesia groups but if other groups want to use it, we can discuss buying more licenses. Please have a look at the Vasp FAQs on licensing then email us.

See the VASP manual for more information and examples.


Vega

is tool that can be useful for volume/cavity, logP and surface calculations. It can also be useful for converting older molecular file formats like BioDock, Quanta/CHARMm, Insight II, MoPac, etc.

The VEGA home page contains more information.

The Windows version is free and has a graphical interface. In the MGCF, we only have the command line version. To use this on the MGCF workstations, type vega_setup first.

Assuming you have a PDB file called sample.pdb, type vega sample.pdb -f info and you will get lots of data on sample.pdb. Use vega -h for more help.


Vesta

is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. It can handle a large number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces and do lattice transformation from conventional to non-conventional. It can visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP. It can do arithmetic operations among multiple volumetric data files and give high quality rendering of isosurfaces and sections.

This is available on the linux workstations (not Tiger). Type vesta to start the program. See the home page for details.


Vista

is for data analysis of searches from the Cambridge Structural Database. It reads files generated by ConQuest when 3D parameters are defined in a CSD search. It displays geometry and other parameters in a spreadsheet format and can make histograms, scattergrams and polar plots, and do statistical analyses like linear regression and principal component analysis.

Like the CSD, this software is available on the linux workstations (not Tiger).

To use Vista, you must specify parameters (bond lengths, angles, etc.) in your Conquest search, which you can access under the 3D menu in Conquest's Draw module. You can access Vista directly from Conquest's View Results panel by clicking on the Analyse Hitlist button. Otherwise, save the search results as a .tab file by selecting File -> Export Parameters and Data, then access Vista from the command line by typing
vista yourfilename (no extension).

VMD

is developed by the Theoretical Biophysics Group at the University of Illinois. It is designed for the visualization and analysis of biological systems such as proteins, nucleic acids and lipid bilayer assemblies. It may be used to view other molecules since VMD can read various standard files. VMD can make publication quality images. For example, see how to make great MO images from Gaussian data.

VMD can animate and analyze trajectory files from molecular dynamics (MD) and can make movies from a series of coordinate frames.

This software is available on the MGCF workstations (not Tiger). Type vmd to start the program.

The software is easy to use but hard to understand at first. The User Guide and Tutorials are excellent so start there.


Voidoo

is older software which detects cavities in macromolecular structures. It is written by Gerard J. Kleywegt at the Uppsala Software Factory.

Voidoo output can be viewed with O or Chimera. Chimera is easier to use but requires conversion of the output data from Voidoo. Use Voidoo to write NewEZD output files. Then use the ccp4 program xdlmapman to convert NewEZD output to CCP4 format. CCP4 format files can be visualized with Chimera's Volume Viewer.

All of these programs are on the linux workstations.

See the home page and Manual for more information.

We also have RAVE from the Uppsala Software Factory. This includes mapman which can convert NewEZD to CCP4 format. Programs and sample files are in /home/mgcf/software-ws/rave.


XCrySDen

XCrySDen is a crystalline and molecular structure visualisation program. It has tools for analysis of properties in reciprocal space such as selection of k-paths in the Brillouin zone for band-structure plots and visualisation of Fermi surfaces.

This is available on the MGCF workstations in the Facility (not Tiger). Type xcrysden to start. See the XCrySDen home page for more information.


xmgrace

xmGrace is a simple XY plotting tool that can do linear and nonlinear curve fitting, arbitrarily complex user-defined fitting functions, FFT, integration and differentiation, histograms, splines, interpolation and smoothing, convolution, correlation, covariation, and sorting.
This is available on the MGCF workstations in the Facility (not Tiger). See the Grace home page for docs, FAQs, and tutorials. Type xmgrace start.


XTB

is an extended tight-binding semi-empirical program for molecules.
This is available on the MGCF workstations in the Facility and on the Tiger cluster. See the home page for docs, FAQs, and tutorials.

We also have MGCF tutorials for XTB.

To use XTB on an MGCF workstation, type xtb_setup to set environment variables for that shell.

To submit jobs to Tiger, login in to any MGCF workstation, cd to the calculation folder (one calulation per folder is advised). Then type:
run_xtb jobname [num_core]
The default num_core (number of cores) is 1.