Computational Chemistry at NIST

These pages have been designed for the purpose of consolidating computing information for the computational chemistry community at NIST.  This page contains:

Software Packages

This list contains the computational chemistry software packages that are available on NIST's high-performance platforms.

Ab-initio programs for electronic structure, energy, geometry optimizations, vibrational frequency calculations are in red.
Molecular Dynamics packages are in brown.
Graphics type packages for visualization are in dark blue.
Utilities are in black.

Click Here for a List of ALL PACKAGES currently supported by ITL.


Ab-intio/Electronic Structure

Name IBM SP/2 Cluster
danube.nist.gov 		SGI Origin 2000
arno.nist.gov
(8 nodes R10K) 		SGI Origin 2000
amur.nist.gov
(32 nodes R10K) 		SGI Origin 2000
neva.nist.gov
(32 nodes R12K) 		SGI Origin 2000
tay.nist.gov
(32 nodes R12K) 		Settings & how to use Comments Internal NIST Example
GAUSSIAN 98 Serial/Parallel Serial/Parallel Serial/Parallel Serial/Parallel Serial/Parallel click here WebSubmit modules available. Yes
GAMESS-US Parallel only Serial/Parallel Serial/Parallel Serial/Parallel Serial/Parallel     no


Molecular Dynamics

Name IBM SP/2 Cluster
danube.nist.gov		 SGI Origin 2000
arno.nist.gov
(8 nodes R10K) 		SGI Origin 2000
amur.nist.gov
(32 nodes R10K) 		SGI Origin 2000
neva.nist.gov
(32 nodes R12K) 		SGI Origin 2000
tay.nist.gov
(32 nodes R12K) 		Settings & how to use Comments Internal NIST Example
UHBD             Brownian Dynamics No
CHARMM             Molecular Dynamics No
Amber             Molecular Dynamics No


Graphics
Name IBM SP/2 Cluster
danube.nist.gov		 SGI Origin 2000
arno.nist.gov
(8 nodes R10K) 		SGI Origin 2000
amur.nist.gov
(32 nodes R10K) 		SGI Origin 2000
neva.nist.gov
(32 nodes R12K) 		SGI Origin 2000
tay.nist.gov
(32 nodes R12K) 		Comments Internal NIST Example
CERIUS2 Only On Public SGI systems On public SGIs Links to outside documents
INSIGHT-II Only On Public SGI systems On public SGIs Links to outside documents
MOLDEN no yes yes yes yes   No
XMakemol no yes yes yes yes   No
RasMol Only On Public SGI systems Type "rasmol" at prompt Links to outside documents


Utilities
Name IBM SP/2 Cluster
danube.nist.gov		 SGI Origin 2000
arno.nist.gov
(8 nodes R10K) 		SGI Origin 2000
amur.nist.gov
(32 nodes R10K) 		SGI Origin 2000
neva.nist.gov
(32 nodes R12K) 		SGI Origin 2000
tay.nist.gov
(32 nodes R12K) 		Comments
WebSubmit yes yes yes yes yes Web based batch job submission

Package Descriptions
 

Cerius2 is a molecular modeling software package that provides a set of modeling, visualization, and computational tools for chemical analysis from Molecular Simulations.   (http://www.msi.com) You can also get a lot of protein structural data to visualize from the PDB web site, http://rcsb.nist.gov. GAMESS Home Page    (http://www.msg.ameslab.gov/GAMESS/GAMESS.html)

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This program is maintained by the members of the Gordon research group at Iowa State University. This software can also be run on Macintosh or PC's.

The Official Gaussian Home Page   (http://www.gaussian.com) is the definitive word on this package. You will find a Gaussian 98 On-line help file, a list of Keywords and Technical Notes,

If you have are a new user or unfamiliar with GAUSSIAN at NIST, please click here for NIST-wide specifications.

If you need help getting started using GAUSSIAN, there are a series of web pages just for you. Please click here.

Insight II is a graphical modeling and simulation environment that seamlessly integrates a wide variety of scientific software for research in the life and materials sciences.
  Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the 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 can write a variety of graphics instructions; tekronix4014, hpgl, postscript, XWindows, hp2392 and Figure. The Xwindows version of Molden is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files. 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 was also submitted to the QCPE (QCPE619), although the Xwindows version is considerably running behind on the current one.
  The UHBD (University of Houston Brownian Dynamics) program is capable of solving the linearized and non-linear Poisson-Boltzmann equation using a finite-difference method. In addition, the program can be used to perform Brownian dynamics calculations for steady and non-steady state rate constants of encounter of a substrate/inhibitor with a target (enzyme). The UHBD code can also be used to perform stochastic dynamics calculations or molecular mechanics energy minimizations using the Poisson-Boltzmann and/or other molecular mechanics forces. The program also has the capability to compute electrostatic free energies of binding of two molecules and can include the non-electrostatic surface area changes and how that affects the energy. Many other more minor methods/capabilities are available.
 

XMakemol is a program for viewing and manipulating atomic and molecular systems, displaying atoms, bonds, and hydrogen bonds. It is written in ANSI C and uses the Xlib library for rendering and also the Xt and Motif toolkits for the user interface. XMakemol is distributed under the GNU GENERAL PUBLIC LICENSE (Version 2, June 1991)

You can get much more information by going to the XMakemol homepage: http://brian.ch.cam.ac.uk/~matt/XMakemol/XMakemol.html
 

RasMol is a free program which displays molecular structure. It is available for on PC/Windows (RasWin), MacIntosh (RasMac), unix, and VAX VMS (the latter two via X-windows), and also (through ports by users) for NEXTSTEP and for Acorn Archimedes RISC OS. RasMol is a powerful educational tool for showing the structure of DNA, proteins and smaller molecules. It is also a powerful research tool. It is easy to use and produces beautiful, space-filling, colored, 3-dimensional images. It is the generous gift to the scientific public of its author, Roger A. Sayle, Ph.D., GlaxoWellcome, and the University of Edinburgh (all in the United Kingdom).
 

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Need data?

NIST's ONLINE Reference Databases
NIST Chem web Book
Protein Data Base    This is a good site especially if you plan on using Cerius2.
Computational Chemistry Comparison and Benchmark DataBase

 

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Links to NIST's CENTRAL COMPUTING Facility

The above link will let you give you information for generic job submission details.

Also check out the Consulting Services if you need additional assistance.

NIST Central Machines
Machine name Hardware
danube.nist.gov A 48 node (80cpu) IBM SP/2
sci-apps.nist.gov IBM workstation cluster
arno.nist.gov An 8 node SGI Origin 2000
amur.nist.gov A 32 node SGI Origin 2000
neva.nist.gov A 32 node SGI Origin 2000
tay.nist.gov A 32 node SGI Origin 2000


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When all else fails..

If you are having a problem using software, getting started using a particular machine or would like to make a request for new software then:

Contact Dr. Robert Bohn of The Information Technology Laboratory ([email protected]) at x-4731. Send me e-mail with a description of the problem, the package and the type of platform you used.

Scientific Applications and Visualization Group
Mathematical and Computational Sciences Division
Information Technology Laboratory
NIST

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