Chemistry, Visualization and Related Software in the MGCF

We have eleven good quality Linux workstations. These are gravel, betty, wilma, stone, bambam, barney, slate, lava, fred, rubble and bronto. These all share the same software suite with a few rare exceptions.

We have a compute cluster called dino that has 48 dual 6-core (AMD-64) nodes, for a total of 576 available cores. The cluster is primarily for computation via a queueing system. Interactive use is discouraged. Many people are not familiar with queueing and we aim to make this as easy as possible. We have shortcut commands for many common programs that 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) linux workstations or 2) dino (the compute server).


ADF (2016)

ADF is a DFT program and can can be applied to isolated molecules, polymers, slabs, solids, molecules in solvents, and molecules in protein environments. It can treat all elements of the periodic table and contains state-of-the-art relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei. Chemically relevant analysis methods are available (including bond energy decomposition, fragment orbitals and charge decomposition). The QM/MM implementation enables the treatment of many thousands of atoms. ADF includes the very latest meta-GGA and hybrid exchange-correlation functionals as well as a full range of standard functionals.

The license for this program is only for the Whaley group but we can add other groups to the license. 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 guidlines which are recommended reading prior to using ADF.

While the adf program runs on any Linux machine in the MGCF, the GUI is only licensed on the workstation named gravel. Either login to the console on gravel or use ssh -X gravel from any other lab workstation. Then type adfinput to start the graphical user interface. Use this to setup and then "Save As" your input files.
On the command line, you can type run_adf to start your job in the queue on dino. ADF generates a series of files with non-unique names so each ADF job should be run from its own sub folder.

See the Documentation page for information and examples.


Aimall

AIMAll performs quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems - starting from molecular wavefunction data. The software implements 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. Please note, this is licensed only on "fred" and "rubble".

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


Amber 14

Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain and are used in a variety of simulation programs); and a package of molecular simulation programs. The major programs in Amber 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 the "main" program used for molecular dynamics simulations, and is also used for 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.
ptraj: is used to analyze MD trajectories.
mm_pbsa: is a script to automate post-processing of MD trajectories.

See the Amber home page for information and examples. To use xleap, etc on the workstations, type "amber_setup" first. That will set the right environment variables for that shell. For simulations on dino, use the run_amber (for sander) and run_pmemd scripts. These setup basic job files which you should check and edit if needed. If the job files look good, then they can be run in the queue on dino. Ask Kathy Durkin for help.


APBS

APBS performs a numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of 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. This software is enabled as a plugin in other programs, plus there are are some online resources. We also maintain a command line version in case it is of use to you.

See the home page for usage instructions. Type apbs to start. This program is on the Linux workstations (not the computing cluster).



Art of Illusion

Art of Illusion is a free, open source 3D modelling and rendering studio. It can create high quality, photorealistic images and animations. A scripting feature allows creation of new types of objects and tools. For information and tutorials, see the home page.

AOI is installed on the Linux workstations (not the computing cluster). Type aoi to start.


Avogadro

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 Linux workstations (not the computing cluster).


Babel

This 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. For more information, see the home page.


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. If there is something you want to use, email Kathy Durkin. Also, these tools are not in your PATH by default. Type: bioinformatics_setup to activate these programs. Activation is for that shell only.

See also R/Bioconductor


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 our linux workstations (not dino). Before using CCP4, you must type: ccp4_setup to activate these programs. Activation is for that shell only.

The list of programs are in /usr/software/ccp4-7.0/bin
See the CCP4 page for documentation.

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


Chemissian

Chemissian is a user-friendly, Windows-based program for analyzing electronic structure and preparing publication-quality orbital energy-level diagrams from HF or DFT wave functions. Diagrams can be annotated and labeled from within the program. 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. It is installed on our Windows virtual machine. The software is Windows only (there is no Mac or Linux client). Email Kathy Durkin if you wish her to set up your login to use a Windows virtual machine in order to start the program. See also our Windows help page.

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

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

This software is installed on the Linux workstations (not the computing cluster). Type chimera to start.


Compilers and Libraries

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

All Linux 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 some 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. Do not edit your .tcshrc 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_gaussian and related scripts to submit calculations, the correct parallel environment will be put in the queue script. If you need to hand configure your own queue script, see the FAQS and/or ask Kathy for help.


Comsol

Comsol can simulate any physical process that can be described with partial differential equations. Problems can be defined in 1D, 2D and 3D.

The program is on the Linux workstations for interactive use.

We have 2 licenses types for Comsol. One is a teaching license (called a Class Kit Lic ense or CKL - shared with a group in the Dept of Nuclear Engineering) and the other is a research license. The CKL is fully featured but allows for 25 simultaneous student users. It includes the modules: COMSOLGUI ACDC CFD HEATTRANSFER LLEXCEL LLMATLAB LLSOLIDWORKS OPTIMIZATION PARTICLETRACING STRUCTURALMECHANICS CADIMPORT CADREADER.

The research license only allows for 2 simultaneous research users. It has all of the same modules as in CKL but also has: CHEM ELECTROCHEMISTRY MEMS MULTIBODYDYNAMICS NONLINEARSTRUCTMATERIALS RAYOPTICS RF SEMICONDUCTOR WAVEOPTICS.

If you are using Comsol for class, start Comsol version 5.2a using the CKL by typing:
comsol_ckl
If you are using Comsol for research, start Comsol version 5.2a using the research license by typing:
comsol_rl
If you just type comsol then you will start Comsol version 5.2a using the CKL.

Older version of the research license are available:
Type comsol51 to start version 5.1 of the program.
Type comsol5 to start version 5.0 of the program.

comsol -help
will show other options.

For more information, see the Comsol site.


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.

This program runs on our linux workstations (not dino). We have an MGCF tutorial and there are CSD documentation and tutorials.

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

There is also a spreadsheet program called Vista for data analysis. Another great CSD related program is Isostar for studying nonbonded interactions in CSD and PDB databases. There are many other CSD programs. Our installation includes Mogul, Mercury and related tools.


Desmond

This is 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. Thus, the graphical interface for Desmond is Maestro. See the documentation.

We have a draft tutorial. This can be run across many processors. Ask for help before submitting large jobs.


Dia

Dia is used to create diagrams such as entity relationship diagrams, UML diagrams, flowcharts, network diagrams, and simple circuits. It is also possible to add support for 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.

This is available on the Linux workstations (not the computing cluster). Type dia to start. For more information, see the Dia home page.


Diamond

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

The software is Windows only (there is no Mac or Linux client). Email Kathy Durkin if you wish her to set up your login to use a Windows virtual machine in order to start the program. See also our Windows help page.

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

For more information, see the Diamond 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. The software is on the workstations (not the server).


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 Linux workstations (not on the server). See the home page for usage information.
Type dftd3 to start.


DMS

DMS is an open source program for computing the molecular surface of a molecule. The surface computed is that defined by F. M. Richards (1977, Ann. Rev. Biophys. Bioeng.). In addition to the molecular surface, DMS can report the molecular surface area associated with each surface point, and surface normals at each surface point. The molecular surface resembles the van der Waals surface of a molecule, except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated. The surface includes cavities in the interior of the molecule, even if they are not accessible to a solvent molecule coming from the outside.

This is available on the Linux workstations in the Facility (not the server). See the UCSF CGL software page for more information. Type dms to start the program.


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. Ask Kathy Durkin for assistance.


FDTD Solutions

FDTD is a High performance 3D FDTD-method (Finite-Difference Time-Domain) Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. We have a very limited number of licenses so please close the program when not in use. Type fdtd to start the program.
This software is available on our Linux workstations.


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. Ask Kathy to configure your login if you want to use this. It runs on our Linux 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 QChem.

This software is available on Linux workstations. Type gabedit to start.


Gamess

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

We have version August 18, 2016 on the workstations, version 2014 on the computing cluster (dino). This cluster will be upgraded in Spring 2017. Gamess is available on all MGCF linux machines but it should primarily be run on the computing cluster (dino). Basic (dual 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 dino.

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 12 core in shared memory so rational num_cpu choices are 6 and 12.

Very short jobs to test inputs may be run on the command line on the linux workstations (not dino):
/usr/software/gamess/rungms exam01 >& exam01.log
assuming your input file is called exam01.inp.

There is no graphical user interface for Gamess, but you might want to consider Avogadro or Gabedit.


Gaussian

This is an electronic structure modeling program with a a wide variety of Hamiltonians and basis sets. Each user of the software is required to sign a license agreement. Contact Kathy Durkin if you wish to use the software in the MGCF and have not yet signed a license agreement.

Gaussian Inc just released a new verion in Feb 2017. We do not have that yet and their entire website has changed. Many of the links below have changed. We plan on buying the new version later this year. In the MGCF, you can find the docs for Gaussian 09 by opening a web page with the url:
file:///usr/software/gaussian/g09.revD01/docs-html/index.htm
Just copy/paste this url into a web browser. This will only work on MGCF computers.

We are running Gaussian09 revision D01. You can submit Gaussian calculations to our server on the command line. For an input file called test001.com you can type:

run_gaussian test001

Gaussview is a graphical interface to set up and review Gaussian calculations. Calculations submitted through Gaussview will automatically be sent to our computing cluster. The default number of cpus is 1 but you can use the Link Tab to request up to 12 cpus. This puts an %nprocshared entry in your input file which is read by the queue and assigned accordingly. You should assign 3.8GB of memory per cpu. 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.

Our FAQS have more details on job submission including how to access older Gaussian versions and how to visualize Gaussian output in other programs. Faq 11 shows how to manually generate cube files.

We have tutorials and a guide on convergence issues, restarting, transition state searches, ONIOM, G3, NBO, and more on nice pictures of your output.

How to make ESP/Density plots.

Many users need custom basis sets.

See also how to deal with thermochemical data from Gaussian.

The tech support page has a guide on plotting UV/Vis Spectra.

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.

opt=modredundant: There is a format change for the opt=modredundant keyword in Gaussian09 C01.
NMR=CSGT calculations require an additional keyword.
Please see our notes for details on these two bugs.

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 Linux workstations in the Facility (not dino). See the home page for usage information. Type gausssum to start.


Gaussview 5.0.8

Gaussview is a graphical user interface for Gaussian09. By default it runs G09 revision D01 (as of 2/5/15).

Gaussview has built in help pages and online documentation.

Click on the Gaussview icon on your Desktop or type gv to start.

Actual Gaussian calculations should be run on our computing cluster. Input files must use a .com extension (not .gjf). The Submit option is to run on our computing cluster by default. You will see an error message about "failed to return a log file". Gaussview becomes disconnected from Gaussian during the job submission to the cluster, so you will always get that message. You can follow your calculation using qstat and you can also load in the current state of the .out or .chk file while the calculation is still running.

Cubegen error: We have noted an problem where Gaussview is not always able to read Gaussian09 C01 or D01 chk files for cubegen. Please see our workaround for rev C01 and rev D01.

opt=modredundant: There is a format change in the opt=modredundant keyword in Gaussian09 C01. Please see our notes.

If you want to change the default version of Gaussian called by Gaussview, go to the menu File - Preferences in Gaussview and then select the Job Setup option. Then change the
run_gaussian @INFILE
to be something like these examples:
run_gaussian.g09d01 @INFILE
run_gaussian.g09c01 @INFILE

Many users need to more basis set options than Gaussview can provide so see our notes on custom basis sets.

Gaussview has the ability to save images under the File menu. If want to make changes, ImageMagick is an nice image editor.

See the FAQS for more image and job submission information. For high quality MO images, see our FAQ. We recommend VMD and have detailed instructions for using VMD with Gaussian data.

If you are connecting remotely from a Mac there may be incompatible display effects with GaussView. A work-around is to type setenv USE_MESAGL immediately before starting GaussView (the gv command). See our FAQS for general instructions on how to connect from a Mac.


GIMP

The GIMP is the GNU Image Manipulation Program. It is suitable for such tasks as photo retouching, image composition and image authoring. It a very like Photoshop with a much lower price (free).
It can be used as a simple paint program, a expert quality photo retouching program, an online batch processing system, a mass production image renderer, a image format converter, etc.

It is on all Linux machines in the Graphics Lab (not dino). Type gimp to start. See the GIMP home page for documentation.


Glide

This is a fast ligand-protein docking program distrubuted by Schrodinger Inc. Glide searches for favorable interactions between one or more ligand molecules and a receptor molecule, usually a protein or a protein and a cofactor. Please read the documentation for more details on the algorithm.

The graphical interface for Glide is Maestro. Type maestro to start the graphics interface (please only do this on the linux workstations, not on the server, dino). Then select Glide from the Applications Menu.

We recommend you start by trying out our tutorial.


gnuplot

This is a command driven interactive plotting function available on the Linux 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 is a tool to visualize chemical properties, total electron densities and molecular orbitals of small molecules. Data from programs such as Jaguar, Gaussian, Gamess, etc. can be analyzed if the output files from these programs have been converted into the .plt-file format understood by gOpenMol. Moreover, dynamics can be visualized and a short mpeg animation of the dynamics files generated.

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 Linux workstations. It is not installed on the server. 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. Note, there were major changes from version 4 to 5 and input files are NOT interchangeable. Online documentation on the web can be confusing since it is often not clear which version is being used. The link above is to the documentation for the version in the MGCF.

Type gromacs_setup to enable use of the program for a single terminal session. Note, as you read online docs, you will see instructions to source XXX/bin/GMXRC. Skip that since it is built into the gromacs_setup command. Also, rather than gmx mdrun --version, we have the mpi version so type gmx_mpi mdrun --version. We have version 2016.2 which was released on 02/07/2017.


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 Linux workstations (not dino). 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.

Documentation and example files are in /usr/software/gulp on the linux workstations. This is not on the server. For more information, see the home page.


HEX

Hex is an interactive molecular graphics program for calculating and displaying feasible docking modes of pairs of protein and DNA molecules. Hex can also calculate small-ligand/protein docking (provided the ligand is rigid), and it can superpose pairs of molecules using only knowledge of their 3D shapes. The main thing which distinguishes Hex from other macromolecular docking programs and molecular graphics packages is its use of spherical polar Fourier correlations to accelerate the docking and superposition calculations.

It is available on the linux workstations and has built in documentation and tutorials. Type hex to start.

For more information, see the Hex web page.

There is a very preliminary intro to docking available for Graphics Lab users.


HMMER

HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.

It is available on the linux workstations. To see how to use HMMER, visit the HMMER home page and ask Kathy Durkin to add this software to your login.


ImageJ

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 Linux workstations. Type imagej to start the interactive program. There is suite of command line tools as well.


ImageMagick

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 Linux workstations.


IQmol

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 available on all of the linux workstations in 175 Tan Hall, not on dino.

Type iqmol to start the program.

For more information, see the home page.


Please note, while IQmol works as a builder for QChem, it is not integrated with the queue on dino so you have to write a input file from IQmol and then use run_qchem on the command line.


Also, you must open the Edit-Preferences Menu and set the Fragment Directory: /usr/software/IQmol-2.5.1/share/fragments and the QChem Database File: /usr/software/IQmol-2.5.1/share/qchem_option.db


Isostar

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 the isostar link.
When prompted for an application with which to open a file, specify /home/csd-2017/IsoStar-2.2.4/isostar/bin/run_isostar

When the new Isostar application opens, under the Options menu, choose Hyperlink Server. Then in the box labelled "IsoStar Server", type: http://glab.cchem.berkeley.edu
In the box labelled "Script", type: /cgi-bin/isostar_server.cgi

If you have troube at this step, ask Kathy for help. Firefox may not recognize the istr file type and we may need to edit the mimeTypes.rdf. For more information see the CCDC.


Jaguar

This 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. From Schrodinger Release 2016-2, you can choose jaguar_dino as the host. The 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 so you will likely close Maestro, logout and come back to review later on or the next day.

To run on the server (dino), you can also choose Write from the Job panel. Then open a Linux terminal, cd to the correct folder and type:
run_jaguar inputfile
where inputfile if the filename.in file you created in the Write step.
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 there is a wait and you just want to do some input testing, you can use:
run_jaguar inputfile debug
This will bypass waiting in the main queue but will only allow runs up to 20 minutes.

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

Note that from Schrodinger Release 2016-4, you must run on the local workstations, not dino. Or, if you really want to run on dino, you must write job files and use the run_jaguar process. This is due to a problem on dino with an incompatibility with Schrodinger Release 2016-4. We are planning to upgrade and/or replace dino in the Spring of 2017.


Jalview

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 Linux workstations (not dino). Type jalview to start the program.


JMol

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 Linux workstations (not the server). Type jmol to start the program.


Knime

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 Linux workstations (not dino). Type knime to start the program.


LAMMPS

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, not on dino.

The executable names are lammps and lammps-openmpi .

For more information, see the home page. There are lots of third party tools for input and analysis. We have TopoTools in our version of VMD. There are sample inputs and tutorials at that page.


Lumerical FDTD

FDTD Solutions is a 3D Maxwell solver, capable of analyzing the interaction of UV, visible, and IR radiation with complicated structures employing wavelength scale features.

FDTD Solutions empowers designers to confront the most challenging photonic design problems. Rapid prototyping and highly-accurate simulations reduce reliance upon costly experimental prototypes, leading to a quicker assessment of design concepts and reduced product development costs. FDTD Solutions can facilitate your success in diverse application areas, from fundamental photonics research to current industrial applications in imaging, lighting, biophotonics, photovoltaics, and many more.

It is available on all of the MGCF linux workstations in 175 Tan Hall and the Kavli workstations in 101 Campbell, not on dino.

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

This is a graphical user interface for a variety of biomolecular and chemistry programs. It is distributed by Schrodinger Inc and the programs it interfaces with include Macromodel, the docking program Glide and the DFT program Jaguar.

We are running 2 versions of Maestro: 2016-2 and 2016-4. Version 2016-2 is Maestro Classic whereas version 2016-4 is the new style Maestro, also called Maestro 11. If you have never used Maestro, use version 2016-4. If you are a regular user of Maestro Classic, allocate a few hours to learn the new version as soon as possible.

When you first open Maestro 2016-4, you may be prompted to review some documentation or Continue to Maestro 11.

We recommend you Continue to Maestro 11. Use a web browser and review the videos: Quick Start and 3D Builder. There are many other videos but often are for Maestro Classic. The underlying algorithms are the same in Maestro Classic and Maestro 11. The difference between Maestro Classic and Maestro 11 is the interface where you select, build, edit, view, import, export, etc. Thus the Maestro Classic vidoes are fine for understanding the power of the program, but you may have to adapt what you see to the context of Maestro 11.

See also the Maestro Quick Reference Card, our tutorials, and the documentation.

While the backend programs Macromodel and Jaguar may be run on dino, the Maestro visual interface should be run only on the Linux workstations.

Type maestro to start version 2016-2 (Maestro Classic). Type maestro11 to start version 2016-4 (Maestro 11). To use Maestro from a remote connection from Windows or Mac, type
maestro -SGL
to start. This bypasses OpenGL and gives a more stable result.

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

Maestro has other skins. The most common used in the MGCF is BioLuminate. If you prefer the BioLuminate skin over Maestro, just type bioluminate to start the program.


Materials Studio

This 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). Each time you start the program, a license must be checked out from our server. Email Kathy Durkin if you wish her to set up your login to use a Windows virtual machine in order to start the program. See also our FAQS.

Modules include Castep and Gulp. More information is available from Biovia (formerly Accelrys).

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


Mathematica 10.0.2

Mathematica is a complete technical computing environment that integrates numeric and symbolic computations, interactive document capabilities, an advanced programming language, graphics system, etc. It is a programming environment for mathematical manipulations and plotting. Simple and sophisticated calculations, polynomials, integrals, etc. are all treated in this program.

We have a network license. When you start the program for the very first time, you will have to identify the license server. When prompted, click the button "Other ways to activate". Then select "Connect to a Network License Server". In the resulting dialog, enter "amanda.math.berkeley.edu" and click "Activate". Upon successful activation, Mathematica will launch and your login will be setup for future access. Type mathematica to start the main program.

*****Mathematica and Matlab both have a subprogram called "mcc". If you type "mcc" you will get Matlab's version! If you want Mathematica's "mcc" on the workstations, you must type either:
/usr/software/Mathematica/10.0/Executables/mcc
or
mcc_mathematica

If you use it on dino in a script, add /usr/software/Mathematica/10.0/Executables to your PATH. Ask for help if this is unclear

Please report back to Kathy Durkin how this works out or if you prefer a different solution.

The Mathematica Book, Edition 5, is available in 175 Tan Hall by request.

Documentation, sample programs, etc are available. See the Mathematica home page for more information.


Matlab

This 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. A graphical interface facilitates use of this software.

Matlab R2016a is available for interactive use on the Linux workstations and most work should be done there. Talk to Kathy about configuring scripts for longer jobs. Dino has an older version for now, while we are awaiting a scheduled operating system upgrade. If you wish to use Matlab on dino, you must use 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

On the Linux workstations, type matlab to start the program.

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

Technical support is available directly from tech@mathworks.com

See the Matlab home page for current information.


Mercury

Mercury is for visualising crystal structures in three dimensions, including: full range of structure display styles, view directions, colours and structure manipulations * location and display of hydrogen bonding and other short contacts * ability to build and visualise a network of contacts * packing diagrams of single and multiple cell contents * measurement and display of geometrical parameters * display of centroids, least-squares mean planes and Miller planes * ability to generate and display slices through a crystal in any direction For more information, see the home page where documentation is available.

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

In recent months we have had an occasional problem where Mercury cannot browse to open files. The problem is related to a misconfigured file somewhere in the /home/username/.config folder. (Note it is .config, not config. The . hides the file from ordinary ls). The fix is to open a terminal and type these commands:
cd
rm .config/Trolltech.conf
Note the terminal must have /home/username as the current working folder so that is what cd does. It moves you back to the main folder in case you had changed to some other location. The rm command deletes the bad settings file. Then close/open mercury. Any settings files will be regenerated.

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


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.


Modeller 9v5

Modeller 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 5.0

Molden is a visualization tool for displaying output from GAMESS, GAUSSIAN, Mopac and many other computational chemistry programs. It is capable of displaying MO's, electron density, and the 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 all Linux (not dino) workstations in the Lab. Type molden to start the program.


Molekel

This is an interactive, 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 Linux workstations (not dino). Type molekel to start the program.

See the home page for information and documentation.



MOPAC

MOPAC2012 is the latest version of the most widely used semiempirical quantum chemistry package. It has PM6 for all the main group elements and transition metals. Experimental and ab initio data from over 9,000 compounds were used to develop the new PM6 method. It can handle extended solids including straight-chain polymers such as bucky tubes (1D), surfaces (2D), and crystals (3D) with periodic boundary conditions. For full details, please see the brochure. This is on the Linux workstations (not dino).

The current manual is online and an ancient local copy is also available in the facility at file:///usr/software/mopac/doc
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 1.4.2

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 to start the program. Right now this is only on the workstations, not dino.

The manual is available.

See the MPB site for current links and more information.


Multiwfn

This 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 dino. We have a local copy of the manual.


NAMD

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. See the NAMD home page for documentation and tutorials. You should probably email Kathy first to request the latest version since there are frequent upgrades and we only use this program infrequently.

You can use the run_namd script to start jobs on dino.

run_namd jobname <number_of_cpus>


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 manual and visit the home page. Example files are available.

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 or Jaguar.


NCIPLOT

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

NWChem is a quantum mechanical program for molecular and periodic systems. NWChem 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).

You can run a single cpu NWChem job with the command:

run_nwchem jobname.nw

Type "run_nwchem" on any MGCF Linux 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 Kathy 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 dino. Avogadro and JMol are on the workstations.


O

This is an older program for Macromolecular Crystallography. You are strongly encouraged to read the A-Z of O on O before using the software.

This software is available on the Linux workstations. Type ono to start the program.
This runs the script: /usr/software/o/bin/lin_ono.
O requires an environment variable to indicate the location of the data directory. Currently this is set to point to:
/usr/software/o/data
If you want to point O to a different data directory, you must type
setenv ODAT /home/yourlogin/your_data_directory
Ask Kathy Durkin for help on setting this value permanently.

A lot of O-related information is available at the home page of the developer.


Orca

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.

This is on the workstations (not the server). Email Kathy Durkin if you wish to set up your login to use this software.

See the Orca home page for more information.


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.

The software is Windows only (there is no Mac or Linux client). Email Kathy Durkin if you wish her to set up your login to use a Windows virtual machine in order to start the program. See also our Windows help page.

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


Phenix

Phenix = Python-based Hierarchical ENvironment for Integrated Xtallography

This software is on the Linux workstations (not dino).
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

PLATON is a versatile, SHELX97 compatible, multipurpose crystallographic tool.

This software is on the Linux systems in the Graphics Facility.
Type platon to start the program.

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


PYMOL

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 Linux (not dino) machines.
Type pymol to start.

More information can be obtained at The PYMOL home page.


Python

The MGCF workstations have Python embedded in the operating system. We are changing to Centos 7 in 2017. Pip and Anaconda are native to Centos 7 but not as useful as the full versions. You can type anaconda or pip to use these tools from the native OS version. To have more control, type anaconda2_setup or anaconda3_setup to redirect your terminal session to the full versions of Anaconda. If you want a Jupyter notebook, you could type anaconda2_setup and then jupyter notebook in a terminal window.

This software is available on our Linux workstations (not the computing cluster) machines.


QCHEM

A highly efficient and comprehensive ab initio quantum chemistry package which includes Hartree-Fock, fast DFT with accurate linear scaling algorithms, a wide range of efficient and unique post-HF correlation methods, and a large number of standard basis sets. Quantum calculations can also be extended with QM/MM and molecular dynamics.

See the Q-CHEM home page and the manual for details. Here is a pdf version.

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

IQMol is free and works on Mac/Windows also. QChem/IQmol Tutorials are available. Also look in the folder /usr/software/qchem_4.4.1/samples for sample input files.

This program runs on dino. From the linux machines in the lab, the command to run a single core job on dino is:

run_qchem jobname
This will start a calculation with Qchem 4.4.2 (as of 01/17/17).

run_qchem expects that there is an input file called jobname.in or jobname.inp in the current working directory. Type run_qchem all by itself without any flags to see how it works. Please see also issues related to running QChem in parallel.

Qikprop

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 Linux machines. The graphical interface for Qikprop is Maestro. Type maestro to start the graphics interface. See also the documentation. This is distributed by Schrodinger.


Quantum Espresso

DFT based electronic-structure calculations including plane waves and pseudopotentials (both norm-conserving and ultrasoft). See the home page for details. To run an input called exam01.in on our server, type:

run_espresso exam01
You can request up to 12 core using
run_espresso exam01 num_core
where num_core is the desired number of core for the job.

There is a GUI called PWgui that can help configure input keywords but much of the configuration will be manual.
Type pwgui to start it.

Ryan Cloke in the Fischer group has a blog post with a worked out example for graphene.

Documentation is in /usr/software/espresso-5.4.0/Doc
Example and test inputs are in:
/usr/software/espresso-5.4.0/tests
/usr/software/espresso-5.4.0/PW/tests
/usr/software/espresso-5.4.0/GWW/examples
/usr/software/espresso-5.4.0/NEB/examples
/usr/software/espresso-5.4.0/PP/examples
/usr/software/espresso-5.4.0/XSpectra/examples
and at other scattered locations in subfolders usually called tests or examples. Sometimes they are embedded in scripts and these typically are called something like run_example. Just look around and copy files back to your home folder before trying to run them. The run_example documents should not be run as is. Open them with a text editor and pull out the actual input data to build your own input.
Executables are in /usr/software/espresso-5.4.0/bin
Psuedopotentials are in the /usr/software/espresso-5.4.0/psuedo
You don't need to copy them. Just specify that folder in your input. Let Kathy know if you need other psuedopotentials.

You *must* write active or temporary files to /scr. Do not use the variable "outdir" in your input file. This will create way 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 input file description to understand keyword usage.

There are good tutorials and lectures linked from here.

It you want to do a quick test of your inputs on a MGCF workstation, first type qe_setup. This will set all of the appropriate environment variables in the current window only.
Then type:
/usr/software/espresso-5.4.0/bin/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 submit to dino normally using run_espresso

Coming Soon! QE is being integrated with Maestro, which will make it easier to use.


R

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 ask Kathy Durkin). These include tools for annotation, array assay, bioinformatics, mass spectrometry, and sets of experimantal data.

For more information, see the Bioconductor home page.


Raster3D

Raster3D is a set of tools for generating high quality raster images of molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

Most users access as a tool from another graphics program like Viewmol or VMD. It can be used directly however. Documentation is available at the Raster3D home page.


Rayshade

Rayshade is an extensible system for creating ray-traced images. Most users access as a tool from another graphics program like Viewmol or VMD. It can be used directly however. Documentation is available at the Rayshade home page.


RCSB-LigandExplorer

A viewer that visualizes Protein Data Bank (PDB) data such as the interactions of bound ligands in protein and nucleic acids structures. Ligand Explorer has options to turn on the display of interactions including hydrogen bonds, hydrophobic contacts, water mediated hydrogen bonds, and metal interactions.
This is available on the linux workstations (not dino). It should auto load in your browser if viewing the PDB site. If not, type ligand_explorer to start the program.


Rosetta Commons

Rosetta 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 already installed on MCGF workstations in the /usr/software/rosetta folder.

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

PyRosetta is also installed as a Python site-package.

For online access to some of these tools, try Robetta Server.


Scilab

Scilab is a free scientific software package for numerical computations in engineering and scientific applications. It includes hundreds of mathematical functions with the possibility to add interactively programs (C, Fortran...). It has sophisticated data structures (including lists, polynomials, rational functions, linear systems...), an interpreter and a high level programming language. Scilab has been conceived to be an open system where the user can define new data types and operations on these data types by using overloading. A number of toolboxes are available with the system: * 2-D and 3-D graphics, animation * Linear algebra, sparse matrices * Polynomials and rational functions * Simulation: ODE solver (ODEPACK) and DAE solver (DASSL) * Scicos: a dynamic systems modeler and simulator * Classic and robust control, LMI optimization * Differentiable and non-differentiable optimization * Signal processing * Metanet: graphs and networks * Parallel Scilab using PVM * Statistics * Interface with Computer Algebra (Maple, MuPAD) * Interface with Tck/Tk * And a great number of contributions in various domains.

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


smplayer

Mplayer is a media player for linux and smplayer is the frontend. It plays most MPEG/VOB, AVI, ASF/WMA/WMV, RM, QT/MOV/MP4, OGG/OGM, VIVO, FLI, NuppelVideo, yuv4mpeg, FILM and RoQ files, supported by many native, XAnim, and Win32 DLL codecs. You can watch VideoCD, SVCD, DVD, 3ivx, DivX 3/4/5 and even WMV movies. Type smplayer to start. Type man mplayer for more information.


Solidworks Professional Research

Solidworks 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 automatically estimate manufacturing costs and help convert imported geometry, and utilities that search designs for errors.

The software is Windows only (there is no Mac or Linux client). Email Kathy Durkin if you wish her to set up your login to use a Windows virtual machine in order to start the program. See also our Windows help page.

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


Spartan

This program 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 following Linux machines:
betty wilma lava stone slate bambam bronto gravel.
Not on: dino fred rubble energy nano barney.

Type spartan to start the program.

See the Spartan home page for details about the program.


Tinker 6.2

Tinker is a package for molecular mechanics and dynamics, with some special features for biopolymers devleped by the Ponder group at Washington University (St. Louis). It can use Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (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 workstations, type "tinker_setup" first. That will set the right environment variables for that shell. See also the folders /usr/software/tinker/examples and /usr/software/tinker/params.

The home page contains more information. Here are some other useful links:
TinkerWiki
Manual
Brief tutorial from UCSB


Vasp 5.3

This 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 group 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 talk to Kathy Durkin.

See the VASP examples for version 5.3 features.


Vega

Vega is a free molecular visualization tool that can be useful for volume/cavity measuring. One very nice feature is that it can read older molecular file formats like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. It can also calculate molecular surfaces (Van der Waals, accessible to solvent and Molecular Electrostatic Potential). It has some molecular mechanics calculation tools including some protein docking features and molecular dynamics trajectory analysis tools. It can also do logP (Broto/Moreau, Ghoose/Crippen, Virtual logP*) and lipole (Broto/Moreau, Ghoose/Crippen) calculations.

The VEGA home page contains more information.

The Windows version is free and has a nice Graphical interface. We have the command line only Linux version.

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

This 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 dino). Type vesta to start the program. See the home page for details.

Viewmol

This is an older 3D visualization program for molecular systems. It can show animation of normal vibrations, draw IR, Raman, and inelastic neutron scattering spectra, draw MO energy level or density of states diagrams, draw basis functions, MO's and electron densities, display of forces acting on each atom, display Miller planes in crystals, perform calculation of thermodynamic properties for molecules and reactions. VIEWMOL can read DISCOVER, DMOL3, GAMESS, GAUSSIAN 9X, GULP, MOPAC, PQS, and TURBOMOLE outputs as well as PDB files. Structures can be saved as Accelrys' car-files, MDL files, and TURBOMOLE coordinate files.

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

Vista

This 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 you can generate simple descriptive statistics, histograms, scattergrams and polar plots; statistical analyses, including linear regression and principal component analysis.

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

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

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 Linux workstations (not dino). 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

Voidoo detects cavities in macromolecular structures. It is an older program, 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 /usr/software/rave.


XCrySDen

XCrySDen is a crystalline and molecular structure visualisation program. It can display isosurfaces and contours superimposed on crystalline structures. It has some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for band-structure plots, and visualisation of Fermi surfaces. XCrySDen also provides a (partial) graphical user interface for the CRYSTAL ab initio program and for PWscf and WIEN2k ab initio programs.

This is available on the Linux workstations in the Facility (not dino). 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 Linux workstations in the Facility (not dino). See the Grace home page for docs, FAQs, and tutorials. Type xmgrace start.