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CTBP Computing: Software
See FAQ for information about
getting specific software installed.
Besides the usual end-user software, several applications are
installed on the CTBP computers. If you are interested in using
software that is not on this list, please contact ctbp-help @
ctbp.ucsd.edu.
Software list by package name
| Package |
Commands |
Paths |
Environment Setup and Notes |
| AMBER v9 |
See exe directory under path |
/soft/linux/pkg/amber |
N/A |
| APBS v0.4.0 |
apbs |
/soft/linux/pkg/apbs/bin |
N/A |
| AutoDock 3.05 |
autodock3 |
/soft/linux/pkg/AutoDock/bin/Linux |
N/A |
| CHARMM v32b1 |
See bin directory under path |
/soft/linux/pkg/c32b1 |
N/A |
| GAMESS |
See bin directory under path |
/soft/linux/pkg/gamess |
N/A |
| Gaussian 03 vB.04 |
g03 |
/soft/linux/pkg/g03 |
N/A |
| Gromacs 3.3.1 |
mdrun |
/soft/linux/pkg/gromacs-3.3.1 |
there are two MPI versions in bin/ directory: mdrun-mpi (MPICH1) and mdrun-mpich2 (MPICH2) |
| Intel
compilers v9.1 |
icc, icpc, ifort |
/soft/linux/pkg/intel/compiler91 |
2 |
| Matlab v6.5.1 (R13SP1) |
matlab |
/soft/linux/bin |
Please run this on the cluster nodes only for any computationally intensive calculations. |
| Multiscale Modeling Tools (MMTSB) |
misc |
/soft/linux/pkg/MMTSB/bin |
N/A |
| NAMD v2.6 |
charmrun namd2 |
/soft/linux/pkg/NAMD |
N/A |
| Rasmol v2.7.1.1 |
rasmol_32BIT |
/soft/linux/pkg/rasmol |
N/A |
| VMD v1.8.3a15 |
vmd |
/soft/linux/pkg/vmd/bin |
N/A |
| Notes: |
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1.
Source iccvars.csh in
/soft/linux/pkg/intel/compiler91/bin to setup proper environment.
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2.
Source ifortvars.csh in
/soft/linux/pkg/intel/compiler91/bin to setup proper environment.
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Please direct any questions or comments related to this web page to
ctbp-help @ ctbp.ucsd.edu
Last modified: May 24 2007 02:27:45 pm.
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