The new release of ACES III, release 3.0.6, has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runacesIII" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

The software package ACES II, release 2.8, has been installed on the Altix 4700. ACES II performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES II for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runacesII" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

The October 2010 version of GAMESS has been installed in the Altix 4700. GAMESS performs ab initio electronic structure calculations. A script, "run_gamess.sh", is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

The hybrid MPI/OpenMP version of MrBayes v3.1.2 by Alexis Stamatakis and Wayne Pfeiffer has been installed on the SGI Altix 4700. Information about this version of MrBayes and how to cite the program can be found at http://wwwkramer.in.tum.de/exelixis/software.html.

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. A script to run the hybrid Mrbayes can be found:

Gaussian 09, Revision B.01 has been installed on all HPC computers. Gaussian provides state-of-the-art computational algorithms for performing advanced electronic structure modeling. A complete description of the capabilities of the popular computational chemistry software can be found by clicking on the above link. A script "g09run" is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

The new release of ACES III, release 3.0.4, has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

The latest version (version 1) of the coupled cluster program CFOUR has been installed on the Altix 4700. CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

GROMACS version 4.0.7 has been installed on the SGI Altix 4700 in the directory /usr/local/apps/gromacs. GROMACS is a molecular dynamics software package, designed biochemical molecules, such as proteins, lipids and nucleic acids. Information, documentation and tutorials can be found on the GROMACS web site.

NAMD version 2.7b2 has been installed on the SGI Altix 4700 in the directory /usr/local/apps/namd. NAMD is a molecular dynamics software package, designed for high performance simulations of large biological molecules. Information, documentation and tutorials can be found on the NAMD web site.

The latest release of ACES III release 3.0.3) has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

The latest version of the coupled cluster program CFOUR has been installed on the Altix 4700. CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

NWChem on the SGI ALTIX 4700 has been upgraded to version 5.1.1. A script for running NWChem can be found in the directory

ACES III (release 3.0.1 is ready July 21, 2009) has been installed on the SGI ALTIX 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

Gaussian 2009 has been installed. A script "g09run" is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

Gamess has been updated to the January 2009 version. A script, "run_gamess.sh", is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

Version 4.4 of DMol3 has been installed on the SGI Altix 4700. A script to setup your DMOl3 jobs for submission to LSF can be found:

Amber version 10 has been installed on the Altix 4700. It is located

scilab-4.1.2 has been installed on coffee.ecu.edu. Scilab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. For more information visit the scilab web page:

The 2008 version of GAMESS has been installed. A script, "run_gamess.sh", generates a job file that you submit to LSF can be found in the directory:

GULP is a program for performing a variety of types of simulation 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). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on 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. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

If you want a graphical interface to GULP, look here:

Version 4.0 of POY has been installed on the SGI Altix 4700. POY is a program for phylogenetic analysis of DNA and other data using dynamic homology. The new executable is

Version 4.3 of Materials Studio has been installed. The script to run the new version of DMol3 on the Altix 4700 can be found:

The latest version of gamess has been installed. This is the March 2007 version.

Gaussian has been upgraded to Revision E.01. This release has some important new features. A description of the changes and additions can be found in the release notes. A script for running Gaussian on the Origin 350 can be found in the directory

Version 4.2 of MaterialsStudio has been installed on the Altix 4700. The modules included are: DMol3, Discover, Amorphous Cell, and Castep. The new script to set up the DMol3 LSF job file can be found