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Available Software

The following scientific packages are installed on Keck Center workstations:

Installed software Version Executable
Amber 18 sander, pmemd, pmemd.cuda
Avogadro 1.0.3 avogadro
APBS 1.5 apbs
BrownDye 2018.5.1 bd_top
CalVR 2013.12.2 CalVR
Cambridge Structural Database 2014 cq
charmm c41b2 charmm
Dalton 2016.2 dalton.x
Dirac 16.0 dirac.x
Gaussian g16.B01 g16
Gaussview 5.0.9 gview.exe
Gromacs 5.1.2 gmx
Kepler 2.4
Matlab 2018a matlab
mgltools 1.5.7r1 pmv
MMV 2.5.0 mmv
moe 2018 moe
MSMBuilder 2.5 misc.
NAMD 2.12 namd2
ORCA 4.0.1 orca
Pymol 2.1.1 pymol
PyRx 0.9
Relion 2.0 relion
Rosetta 3.5
Schrodinger 2018 maestro
vina 1.1.2 vina
VMD 1.9.3 vmd

How to use it

The modules package is used to manage, enable and configure scientific applications on the Keck Center workstations. To see what software is available run the following command:

 module avail

you should see something similar to this:

# module avail
------------------------------------------- /soft/etc/modules -------------------------------------------
amber/14(default)             gromacs-cuda/5.0-gcc(default) openmpi/1.6.2
apbs/1.4                      gromacs-cuda/5.0.4-gcc        openmpi/1.6.5(default)
autodock/4.2.6                intel/12.1.5                  openmpi-gcc/1.6.2
browndye/2016.2.5(default)    kepler/2.4                    orca/2.9.1
calvr/2013.12.2               matlab/2013b(default)         orca/3.0.0
chem185/1.0                   mgltools/1.5.7r1(default)     orca/3.0.1
csds/2014                     mmv/2.5.0                     orca/3.0.2
cuda/5.0.35(default)          moe/2013                      orca/3.0.3(default)
cuda/5.5.22                   moe/2014(default)             pymol/1.5
gaussian/g09.a02              msmbuilder/2.5                pyrx/0.9
gaussian/g09.c01              msms/2.6.1                    rosetta/3.5
gaussian/g09.d01(default)     namd/2.10                     schrodinger/2015u4
gaussview/5.0.9               namd/2.11(default)            schrodinger/2016u1
gcc/4.9.3                     namd-cuda/2.10                schrodinger/2016u2
glove/2015                    namd-cuda/2.11(default)       schrodinger/2016u3(default)
gromacs/4.6b2-gcc             namd-cuda/2.9                 vina/1.1.2
gromacs/4.6b2-icc             nbo/6.0                       vmd/1.9.1
gromacs/5.0-gcc(default)      nvidia/4.2.9                  vmd/1.9.2(default)
gromacs/5.0-intel             nvidia/5.0.35(default)
gromacs-cuda/4.6.1-gcc        nvidia/5.5.22

To actually use one of the installed application you need to load the application's environment first and then start the application. For example, to run pymol you need to execute these two steps:

module load pymol

To get help about the package:

module help namd

You can find more information about the modules management package on this help page. Also here is the module man page.

Application specific notes


Before running the CUDA enabled version of pmemd you need to initialize your environment with these two commands:

module load amber/16
module load cuda/7.5.18

Cambridge Structural Database

To use CSDS execute the following:

module load csds


If you want to run Gaussian or Gaussview you have to be added to the Gaussian unix group - please contact for assistance.

Running non-interactive long jobs

The Keck II workstations can be used to run non-interactive, long, computationally intensive jobs. All these jobs must be submitted through the SGE queue manger. More information can be found here.

wiki/software.txt · Last modified: 2018/10/10 08:36 by admin