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Software

Table of Contents

Scientific Web Portals

iNquiry (Bioinformatics)

  • Bioinformatics Web Portal.

SeqWeb (Bioinformatics)

  • The SeqWeb portal provides web access to the Accelrys GCG Package.

WebMO (Chemistry)

Scientific/Engineering Packages

ADF (Computational Chemistry)

  • The Amsterdam Density Functional (ADF) package is software for first-principles electronic structure calculations (molecules and solids), based on Density Functional Theory (DFT). Runs in parallel under MPI.
  • Usage Notes:
    • Available Versions:
      module avail adf
    • Load the module:
      module load adf
      and the environment variable $ADFHOME will then be defined:
      • $ADFHOME/examples (sample input file)

AMBER (Computational Chemistry)

  • AMBER (Assisted Model Building and Energy Refinement)
  • A suite of programs designed to carry out molecular dynamics simulations, particularly on biomolecules.
  • Usage Notes:
    • Available Versions:
      module avail amber
    • Load the module:
      module load amber and the environment variable $AMBERHOME will then be defined:
      • $AMBERHOME/examples (sample input files)
      • $AMBERHOME/doc (documentation, including full manual)

AUTODOCK (Computational Chemistry)

  • Suite of automatic docking tools.
  • Usage Notes:

BABEL (Molecular Modeling)

  • A utility program for converting between file formats used in molecular modeling.
  • Usage Notes:
    • Load the module:
      module load babel
    • babel -help will list available formats
    • babel -m for the menu interface

BLAST (Sequence Analysis)

  • The Basic Local Alignment Search Tool finds regions of local similarity between sequences.
  • A web interface for BLAST is available through the iNquiry Web Portal.
  • Usage Notes:

MPI-BLAST (Sequence Analysis)

UCSC BLAT (Genome Browser)

  • Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. The index – which uses less than a gigabyte of RAM – consists of all non-overlapping 11-mers except for those heavily involved in repeats.

Cadence (Computer Chip Design)

  • Suite of chip design packages.
  • Usage Notes:
    • Available to UB Computer Science and Electrical Engineering Department.
    • Load the module: module load cadence

CFX (Computational Fluid Dynamics)

  • Computational fluid dynamics package.
  • Usage Notes:
    • Available to UB Department of Mechanical Engineering.
    • Load the module: module load cfx
    • CFX tutorial

CHARMM (Computational Chemistry)

  • CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It can perform molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation (including Ewald and PME methods) and periodic images.
  • Some selected features:
    • potential energy functions in CHARMM have been specially parameterized for simulations of proteins, nucleic acids and lipids.
    • energy minimization, normal modes and crystal optimizations
    • Free energy methods for chemical and conformational free energy calculations
    • many types of constraints, including fixed atoms, atomic, NOE, dihedral and internal coordinates
  • Licensing:
    CHARMM is made available to academic users as source code, plus documentation and test input scripts, through Martin Karplus' group at Harvard University. A license for CHARMM can be obtained by writing to: 
    Professor Martin Karplus
Department of Chemistry
Harvard University
12 Oxford Street
Cambridge, MA 02138
  • CCR offers CHARMM for the use of all currently licensed users - please contact ccr-help to confirm your license status.

CNS (Spectra Analysis)

CPMD (Molecular Dynamics)

  • CPMD (Car-Parrinello Molecular Dynamics) is an ab initio electronic structure and molecular dynamics package.
  • Usage Notes:

CS-ROSETTA (Sequence Analysis)

  • CS-ROSETTA is a suite for chemical shifts based protein structure prediction using ROSETTA (Rosetta Commons)
  • Usage Notes:
    • This application is 32 bit.
    • Load the module for 32 bit codes: module load use.32bit
    • Load the module: module load cs-rosetta
    • Documentation available on u2 cluster in /util32/cs-rosetta/v2008.03.18.1/docs
    • Examples available on u2 cluster in /util32/cs-rosetta/v2008.03.18.1/examples
    • Online Documentation

Dalton (Computational Chemistry)

  • Dalton is a program for the calculation of molecular properties with SCF, MP2, MCSCF or CC wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations.
  • Usage Notes:
    • Load the module:
      module load dalton
    • To see the location of a sample calculation, use:
      module help dalton

deMon (Computational Chemistry)

  • A software package for density functional theory (DFT) calculations.
  • Usage Notes:

DOCK (Computational Chemistry)

  • Program that identifies low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor.
  • Usage Notes:

Dynalign (Sequence Analysis)

  • Package to predict the secondary structure common to two (unaligned) RNA sequences.
  • Usage Notes:
    • Load the module: module load dynalign

ESPRESSO (Quantum Chemistry/Physics)

  • Quantum ESPRESSO is a PWscf electronic structure package.
  • Usage Notes:

GAMESS (Computational Chemistry)

  • The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package, distributed and maintained by the Gordon group at Iowa State University.
  • A web interface for GAMESS is available through the WebMO Portal.
  • Usage Notes:
    • Load the module:
      module load gamess
      and the environment variable $GAMESS_DIR will then be defined:
      • $GAMESS_DIR/rungms (GAMESS run script)
      • $GAMESS_DIR/.DOC* (documentation, in plain text - PDFs available on GAMESS web site)
      • $GAMESS_DIR/pbsGAMESS (sample GAMESS PBS script)
    • To list version information, links to more documentation:
      module help gamess

GAUSSIAN94 (Computational Chemistry)

  • A common software package with significant computational chemistry capability. A high performance code (runs in parallel only in shared memory, not across nodes).
  • Revision E.2
  • A web interface for GAUSSIAN94 is available through the WebMO Portal.
  • Usage Notes:
    • Portland Group Fortran - SMP Parallel version:
      • load the module:
        module load g94

GCG (Sequence Analysis)

  • An integrated software package of routines to access, manipulate, and analyze nucleotide and protein sequences.
  • A web interface for GCG is provided by SeqWeb Web Portal.
  • Accelrys GCG Package programs meet a broad range of research needs and can be categorized as follows:
    • Comparison
    • Database Searching and Retrieval
    • DNA/RNA secondary Structure
    • Editing and Publication
    • Evolution
    • Fragment Assembly
    • Gene Finding and Pattern Recognition
    • Importing and Exporting
    • Mapping
    • Primer Selection
    • Protein Analysis
    • Translation
    • Utilities
  • Usage Notes:
    • Available on the command line: The command line interface enables you to run programs from the UNIX system prompt. Each program requires specific information to run successfully. When you run a program, it prompts you for an input file or asks you to answer questions with a yes or no or fill in a number or letter from an menu of available choices. Login using an ssh client to hatfield.ccr.buffalo.edu. To request a CCR account, fill out the Account Request form and select "Bioinformatics System" as the account type.
    • GCG Users Manual

HMMER (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. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
  • A web interface for HMMER is available through the iNquiry Web Portal.
  • Usage Notes:
    • Available Versions:
      module avail hmmer
    • Load the module:
      module load hmmer/version
      and the commands and man pages will be enabled for your environment.

MPI-HMMER (Sequence Analysis)

  • MPI-HMMER is a multiple-level optimization of the original HMMER 2.3.2 code that consists of two distinct optimizations: a portably tuned P7Viterbi function as well as an MPI implementation. The MPI implementation exhibits excellent speedups over the base PVM implementation available with HMMER. Further, a verification mode in both hmmpfam and hmmsearch is provided that ensures (at a cost of speed) results are returned in exactly the same order as the serial version.
  • Usage Notes:
    • Available Versions:
      module avail mpi-hmmer
    • Load the module:
      module load mpi-hmmer/version
      and the commands and man pages will be enabled for your environment.

HYPHY (Phylogenic Analysis)

  • HyPhy (Hypothesis Testing Using Phylogenies) is a software package intended to perform maximum likelihood analyses of generic sequence data and equipped with tools to test various statistical hypotheses.
  • Usage Notes:
    • Serial and parallel versions of the software are installed on the U2 cluster.
    • A GUI (graphical user interface is available.
    • Sample PBS scripts are in /util/HYPHY.
    • List available modules: module avail hyphy
    • Load the module: module load hyphy/version
    • Online Manual

Ingenuity Pathways Analysis (Bioinformatics)

  • Ingenuity Pathways Analysis is a software application that enables biologists and bioinformaticians to identify the biological mechanisms, pathways and functions most relevant to their experimental datasets or genes of interest.
  • Usage Notes:
    • Users run this application through their browser via the Ingenuity website.
    • Users can request an account through the Ingenuity website.
    • For users with existing accounts, click HERE to login
    • NOTE: Users must be on the buffalo.edu or roswellpark.org networks to access the appropriate license information.

MEEP (Computational Physics)

  • MIT Electromagnetic Equation Propagation (MEEP) package is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
  • Usage Notes:

MOPAC (Quantum Chemistry)

  • MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry package.
  • Usage Notes:

MPB (Computational Physics)

  • MIT Photonic-Bands (MPB) is a package to compute definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures.
  • Usage Notes;

MrBayes (Sequence Analysis)

  • MrBayes is a parallel program for the Bayesian estimation of phylogeny.
  • A web interface for MrBayes is available through the iNquiry Web Portal.
  • Usage Notes:

NAMD (Molecular Dynamics)

  • Scalable molecular dynamics package.
  • Usage Notes:

NetCDF (Data Sharing Tool)

NMRPipe (Spectral Analysis)

  • NMRPipe is spectral processing and analysis package.
  • Usage Notes:
    • This application is 32 bit.
    • Load the module for 32 bit codes: module load use.32bit
    • Load the module: module load nmrpipe
    • man pages available on u2 cluster
    • Online documentation

NWChem (Computational Chemistry)

  • A massively parallel software package with a wide array of computational chemistry functionality. A high performance code. Ability for both QM, QM/MM calculations.
  • A web interface for NWChem is available through the WebMO portal.
  • Please read carefully the information in the NWChem listing for a proper citation.
  • Usage Notes:
    • Available Versions:
      module avail nwchem
    • Load the module:
      module load nwchem/version
      and the environment variable $NWCHEM_HOME will then be defined:
      • $NWCHEM_EXEC (binary)
      • $NWCHEM_HOME/pbsNW (sample PBS script)

PAML (Sequence Analysis)

  • A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
  • Usage Notes:

Phred and Phrap (Sequence Assembly Software)

  • Usage Notes:
    • Currently available under Solaris. Please email ccr-help at ccr.buffalo.edu for an account.
    • Detailed information can be found HERE

PHYLIP (PHYLogeny Inference Package)

PHYLIP is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data type that can be handled include molecular sequences, gene frequencies, restriction sites, and distance matrices

  • Usage Notes:

PhyML (Phylogenic Analysis)

  • PHYML is a software package that estimates phylogenies by maximum likelihood.
  • Usage Notes:
    • Serial and parallel versions of the software are installed on the U2 cluster.
    • Sample PBS scripts are in /util/PhyML.
    • List available modules: module avail phyml
    • Load the module: module load phyml/version

PrepMS (Spectra Analysis)

  • PrepMS is a graphical package for MS data preprocessing, peak detection, and visual data quality assessment.
  • Usage Notes:
    • Load the module: module load prepms

Q-Chem (Computational Chemistry)

  • Quantum chemistry package.
  • A web interface for Q-Chem is available through the WebMO portal.
  • Usage Notes:

R (Statistical Analysis)

  • Software environment for statistical computing and graphics.
  • A web interface for R is available through the iNquiry Web Portal.
  • Usage Notes:
    • Load the module: module load R
    • R manuals
    • Rmpi, an Interface to MPI (Message-Passing Interface), is available with R-2.6.2 on the u2 cluster. A sample PBS script is in /util/R.

Rosetta (Sequence Analysis)

  • Rosetta Commons is a protein sequence analysis suite.
  • Usage Notes:
    • This application is 32 bit.
    • Load the module for 32 bit codes: module load use.32bit
    • Load the module: module load rosetta
    • Documentation available on u2 cluster in /util32/rosetta/v2.2.0/rosetta_documentation
    • Online User Guide

SAGE (Statistical Analysis)

  • SAGE (Statistical Analysis for Genetic Epidemiology) is a collection of statistical analysis packages.
  • Usage Notes:

SOLAR (Sequence Analysis)

  • SOLAR (Sequential Oligogenic Linkage Analysis Routines) is a software package for genetic variance components analysis.
  • Usage Notes:

Star-CD (Computational Fluid Dynamics)

  • Computational fluid dynamics package.
  • Usage Notes:
    • Available to the UB Mechanical Engineering Department.
    • Load the module: module load starcd

STRUCTURE (Sequence Analysis)

  • Package using multi-locus genotype data to investigate population structure.
  • Usage Notes:
    • Load the module: module load structure
    • [ structure manual|http://pritch.bsd.uchicago.edu/software/structure22/readme.pdf]

TINKER (Molecular Modeling)

  • Molecular modeling package.
  • Usage Notes:

Towhee (Computational Chemistry)

  • Monte Carlo molecular simulation package.
  • Usage Notes:

Turbomole (Quantum Chemistry)

  • Quantum chemistry package for ab initio electronic structure calculations.
  • Usage Notes:
    • Load the module:
      module load turbomole
    • For additional usage instructions/tips (especially for execution in parallel):
      module help turbomole

VectorNTI (Sequence Analysis)

Compilers

GNU Compilers

  • The entire GNU compiler suite is available, with the usual invocations, gcc, g++, g77

Portland Group (PGI) Compilers

  • The Portland Group compilers, a suite of high performance compilers and associated tools
  • Usage Notes:
    • For a list of available versions:
      module avail pgi
    • To load desired version (the latest should be the default version) into your environment:
      module load pgi/version
      (e.g. commands for the compiler front-ends, pgcc (C), pgCC (C++),pgf77 (FORTRAN 77), pgf90 (FORTRAN 95), and their man pages).
    • For more information and links to additional documentation:
      module help pgi/version
    • Note that the PGI compilers are compatible with object code produced by the GNU compilers - use the flag -g77libs to ensure compatibility under pgf77 and pgf90.
    • The PGI suite includes pgdbg, a graphics enabled debugger, as well as pgprof, a sophisticated profiling tool capable of line-level profiling.

Intel Compilers

  • The Intel compiler suite, including C/C++ (icc/icpc) and Fortran 77/95 (ifort in version 8, ifc for versions prior to that).
  • Usage Notes:
    • For a list of available versions:
      module avail intel
    • To load desired version (the latest will not always be the default version) into your environment:
      module load intel/version
      (e.g. commands for the compiler front-ends, icc (C/C+), ifort (FORTRAN 77/95, version 8.0), ifc (FORTRAN 77/95, versions 7.1-), and their man pages).
    • For more information and links to additional documentation:
      module help intel/version

Numerical/Message Passing Libraries

HDF

  • Hierarchical Data Format, from NCSA, is a portable self-describing binary format for scientific and engineering applications.
  • Includes I/O libraries and tools for analyzing, visualizing, and converting scientific data.
  • Sample Makefiles and a tutorial are available on the NCSA HDF site.
    • For available versions:
      module avail hdf
    • For detailed usage notes and pointers to more documentation:
      module help hdf/version

MATLAB

  • MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation.
  • Documentation available at the Mathworks website.
  • CCR currently has only a few of the many available toolboxes - if you wish to acquire additional toolboxes, please contact us.
  • Usage Notes:
    • For available versions:
      module avail matlab
    • For detailed usage notes and pointers to more documentation:
      module help matlab/version

MPI

  • MPICH (v1.2)
    • Uses standard (fast or gigabit, depending on platform) ethernet via the ch_p4 device.
    • Full implementation of MPI 1.2 specification, including MPI-2 I/O features of ROMIO and C++ bindings.
    • Given incompatibilities between compilers, we provide versions for each compiler that we support (GNU, PGI, Intel).
    • MPICH provides compiler "wrappers" (mpicc,mpiCC/mpicxx,mpif77,mpif90) for aiding in building codes (finding libraries, header files, etc.). These wrappers accept the same flags as the regular compilers, as well as MPICH specific flags.
    • Usage Notes:
      • To show a list of available compiler/version combinations:
        module avail mpich
      • To set your environment for compiler and version (note that leaving out the version should default you to the latest):
        module load mpich/compiler-version/ch_p4/mpich-version
      • For detailed information and links to more documentation:
        module help mpich/compiler-version/ch_p4/mpich-version
      • For compiler-version, you can substitute any available combination listed by the "module avail mpich" output - note that GNU, PGI, and Intel compilers (often several different versions to support some legacy applications) should all be listed. You should now have mpif77, mpif90, mpicc, mpiCC, mpirun in your $path and $MANPATH. To run your code, use the mpirun task launcher, e.g. in a batch job:
        mpirun -machinefile $PBS_NODEFILE -np 16 ./a.out
        or use the mpiexec task launcher, which is integrated with PBS (but only available within a PBS batch job):
        mpiexec ./a.out
  • MPICH-MX (v1.2)
    • Uses high-performance Myrinet via the ch_mx device.
    • Full implementation of MPI 1.2 specification, including MPI-2 I/O features of ROMIO and C++ bindings.
    • Given incompatibilities between compilers, we provide versions for each compiler that we support (GNU, PGI, Intel).
    • MPICH provides compiler "wrappers" (mpicc,mpiCC/mpicxx,mpif77,mpif90) for aiding in building codes (finding libraries, header files, etc.). These wrappers accept the same flags as the regular compilers, as well as MPICH specific flags.
    • Usage Notes:
      Using Modules Interface:
      • To show a list of available compiler/version combinations:
        module avail mpich
      • To set your environment for compiler and version (note that leaving out the version should default you to the latest):
        module load mpich-mx/compiler-version/ch_mx/mpich-mx-version
      • For detailed information and links to more documentation:
        module help mpich-mx/compiler-version/ch_mx/mpich-mx-version
      • For compiler-version, you can substitute any available combination listed by the "module avail mpich" output - note that GNU, PGI, and Intel compilers (often several different versions to support some legacy applications) should all be listed. You should now have mpif77, mpif90, mpicc, mpiCC/mpicxx, mpirun.ch_mx in your $path and $MANPATH. To run your code, use the mpirun.ch_mx task launcher, e.g. in a batch job:
        mpirun.ch_mx -machinefile $PBS_NODEFILE -np 16 ./a.out
        or use the mpiexec task launcher, which is integrated with PBS (but only available within a PBS batch job):
        mpiexec ./a.out

OpenMP

  • Open Specification for Multi Processing
  • OpenMP is an application programming interface (API) intended for directing multi-threaded shared memory parallelism.
    • Compiler directives
    • Run-time library routines
    • Environmental variables
  • OpenMP is specified for C/C++ and Fortran compilers.
    • Intel
    • PGI
    • GNU (versions 4.1 and greater).
  • Usage Notes:
    • Load the Intel or PGI module.
    • Compile the code with the OpenMP flag.
      • Intel: -openmp
      • PGI: -mp
      • GNU: -fopenmp

Optimized Mathematics Libraries (BLAS/LAPACK/FFT)

  • Intel cluster MKL (Math Kernel Library)
    • For available versions (later versions are generally better performing):
      module avail/mkl
    • For usage, see:
      module help mkl/version
    • Provides highly tuned BLAS, LAPACK, DFTs (discrete fourier transforms), and, in later versions, sparse solvers (PARDISO).
    • The Cluster MKL (versions 7-10) also provides BLACS and ScaLAPACK compiled for MPI over Myrinet.
    • Multithreaded.
    • User Manuals - Chapter 2 provides a Getting Started guide:
  • ATLAS (Automatically Tuned Linear Algebra Subroutines)
    • For available versions (later versions are generally better performing):
      module avail blas/atlas/version
    • For usage, see:
      module help blas/atlas/version
    • Includes Basic Linear Algebra Subroutines, Levels 1-3, highly tuned.
    • A complete LAPACK library is provided, with some routines also tuned for performance.
    • Multithreaded versions are available - see the "module help" listings.
  • Goto BLAS
    • Hand tuned Levels 1-3 BLAS routines from Kazushige Goto.
    • For available versions (later versions are generally better performing):
      module avail blas/goto/version
    • For usage, see:
      module help blas/goto/version
  • FFTW (Fastest Fourier Transform in the West)
    • FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
    • Usage Notes:
      • FFTW should be installed in default locations
      • For detailed usage notes and documentation, see the FFTW website.

PETSc

  • Portable Extensible Toolkit for Scientific Computation (PETSc).
  • PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.
  • Extensive tutorials and a manual available online (also available locally).
  • Usage Notes:
    • For available versions:
      module avail petsc
    • To load desired version into your environment:
      module load petsc/version
      Should set both $PETSC_DIR and $PETSC_ARCH.
    • To show details about PETSc configuration, and links to more documentation:
      module help petsc/version

Visualization & Miscellaneous Packages

IDL (Data Visualization)

  • IDL (Interactive Data Language) is a popular commercial package for data visualization and analysis
  • Built-in library of math, statistics, image and signal processing routines
  • GUI building toolkit
  • Supports a very large variety of data formats, type, and size
  • Usage Notes:
    • For a list of available versions:
      module avail idl
    • For detailed information on each version and links to more documentation:
      module help idl/version
    • To load the desired version into your environment:
      module load idl/version

Java

  • The Java Execution and Development Environments.
  • A complete toolkit for running and developing Java applications and applets
  • Usage Notes:
    • For a list of available versions:
      module avail java
    • For detailed information on each version and links to more documentation:
      module help java/version
    • To load the desired version into your environment:
      module load java/version

Molekel (Molecular Visualization)

  • Molecular visualization.
  • Usage Notes:
    • Load module: module load molekel
    • Requires X-Display.

Tecplot (Fluid Dynamics Visualization)

  • CFD and numerical simulation visualization package.
  • Usage Notes:
    • Must have own license.
    • Requires X-Display.
    • Load module: module load tecplot

TotalView (Parallel Debugging Tool)

  • TotalView is the premier parallel debugging tool for complex applications using MPI and OpenMP APIs.
  • For documentation, tutorials and much more info, go to TotalView Support.
  • Usage Notes:
    • For a list of available versions (you will almost certainly want the latest version, however, which may not be the default):
      module avail totalview
    • To load the desired version into your environment (no version to accept the default):
      module load totalview/version
    • For more information:
      module help totalview/version
    • (Current CCR license can be used by up to 2 concurent users on 8 processors)

VMD (Molecular Visualization)

  • A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
  • Uses OpenGL to provide high-performance 3D graphics.
  • Integrated with babel, which can read molecular data files from CHARMM and X-PLOR as well as PDB files.
  • Can export displayed graphics to files which may be processed by a number of popular ray tracing and image rendering packages, including POV-Ray.
  • Usage Notes:
    Load the vmd module to set your environment:
    module load vmd
    and then bring up the GUI with the vmd command.

Center for Computational Research - University at Buffalo - State University of New York