| Package | Commands | Paths | Notes |
|---|---|---|---|
| AMBER v10 | See bin.* directories under path | /soft/linux/pkg/amber10/ | These directories contain 64bit code |
| APBS v1.1.0 | apbs | /soft/linux/pkg/apbs-1.1.0/bin | |
| AutoDock 3.05 | autodock3 | /soft/linux/pkg/AutoDock/bin/Linux | N/A |
| CHARMM v32b1 | See bin directory under path | /soft/linux/pkg/c34b2 | N/A |
| GAMESS | See bin directory under path | /soft/linux/pkg/gamess | N/A |
| Gaussian 03 vB.04 | g03 | /soft/linux/pkg/g03 | (1) |
| Gromacs 3.3.3 | mdrun | /soft/linux/pkg/gromacs | there are two MPI versions in bin/ directory: mdrun-mpi (MPICH1) and mdrun-mpich2 (MPICH2) |
| Intel compilers v10.1 | icc, ifort | /soft/linux/pkg/intel/intel-10.1 | N/A |
| Multiscale Modeling Tools (MMTSB) | misc | /soft/linux/pkg/MMTSB/bin | N/A |
| NAMD v2.6 | charmrun namd2 | /soft/linux/pkg/NAMD | N/A |
| Python 2.6 | python | /soft/linux/pkg/python-2.6/bin | 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
Please note that MPI (parallel) applications need to be launched with /opt/openmpi/bin/mpirun.
export g03root=/soft/linux/pkg . $g03root/g03/bsd/g03.profile
Unless stated otherwise use /soft/linux/pkg/openmpi/bin/mpirun to launch the application. For more info see SGE scripts examples.
This is under construction, thanks for being patient
| Package | Commands | Paths | Notes |
|---|---|---|---|
| Gromos | See subdirs under path | /soft/linux/Gromos-RH5.intel.openmpi/ | See note (1) |
* (1) To use Gromos, please add LD_LIBRARY PATH:
In bash: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/soft/linux/Gromos-RH5.intel.openmpi/gsl/lib:/soft/linux/Gromos-RH5.intel.openmpi/gromosXX-openmpi/lib
*(1)
test