scientific codes running in the e1350, blue gene/P and sun cluster

Code

version

directory

Notes

ABINIT

6.0.3

/CHPC/usr/local
/BGP/abinit-6.0.3

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within density functional theory (DFT) using pseud. For more info about this package click HERE.

FFTW

3.2.2

/CHPC/usr/local
/BGP/fftw-3.2.2-double

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size and both real and complex data as well as of even/odd data, i.e the discrete cosine/sine transforms. For more info about this libraries click HERE.

GROMACS

4.0.7

/CHPC/usr/local
/BGP/gromacs-4.0.7

Classical molecular dynamics, i.e. simulate the newtonian equations of motion for systems with hundreds to millions of particle. It is primarily designed for biomolecular systems such as proteins and lipids. For more info about this code click HERE and to see the script for running GROMACS in the Sun, e1350 and BG/P systems, click HERE.

VASP

4.6

Per user license

VASP is an ab-inition quantum-mechanical molecular dynamics (MD) using pseudopotentials and plane wave basis set. For more info about this code click HERE and to see the script for running VASP in the Sun, e1350 and BG/P systems, click HERE.

DL_poly

3.07 and
3.09

/CHPC/usr/local
/BGP/dlpoly

A general purpose serial and parallel Molecular dynamic simulation package,This version of Dl_poly has a wider range of structure optimisation features to help with setting up the starting configuration, for more info about this code click HERE and to see the script for running DL_poly_3.07 and 3.09 in the Sun, e1350 and BG/P systems, click HERE.

Code

version

directory

Notes

GROMACS

4.0.5

/opt/gridware
/gromacs

A molecular dynamics package primarily designed for biomolecular. For more information, click HERE.

DL_poly

3.07,
2.18

/opt/gridware
/dlpoly

A general purpose serial and parallel Molecular dynamic simulation package, this version of Dl_poly has a wider range of structure optimisation features to help with setting up the starting configuration. For more info about this code click HERE and to see the script for running DL_poly_3.07 and 2.18 in the Sun, e1350 and BG/P systems, click HERE.

EMBOSS

6.2.0

/opt/gridware
/EMBOSS

EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information about this package, click HERE.

ATLAS

3.9

/opt/gridware
/atlas3.9

ATLAS is an Automatically Tuned Linear Algebra Software. For more information about this software, click HERE.

GAUSSIAN

g09

/opt/gridware
/gaussian

Gaussian is a structure calculation software. For more information about this software, click HERE and to see the script for running GAUSSIAN in the Sun, e1350 and BG/P systems, click HERE.

SEADAS

6.1

/opt/gridware
/SeaDas

SEADAS is a comprehensive image analysis package. For more information about this package, click HERE.

Code

version

directory

Notes

EMBOSS

6.3.1

/GPU/opt/emboss-intel-new

Intel Compilation: EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information on how to run EMBOSS on the GPU cluster HERE

EMBOSS

6.3.1

/GPU/opt/emboss-gcc-6.3

GCC Compilation: EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information on how to run EMBOSS on the GPU cluster HERE

NAMD

2.8

/GPU/opt/namd/NAMD_2.8_Source/

NAMD is a free-of-charge molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems (millions of atoms) HERE