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CPMD (QMMM version) plane-wave/PP quantum CP and BO dynamics.
Usage: mpirun -n NCPUS cpmd.x JOB PATH-TO-PPs >& JOB.out &
mpirun should be set to /opt/openmpi/tcp-gnu/bin/mpirun in your .bashrc
NCPUS number of cpus
JOB name of job file to be executed
PATH-TO-PPs the path to a pseudo potential library (see for eg /home/gpw501/software/cpmd/pseudos/ )
JOB.out name of output file

see: http://www.cpmd.org/^{Image Added} for more details

Amber10 amber molecular dynamics program.
see amber manual for usage executables are located in /home/gpw501/software/amber10/exe/
see http://ambermd.org/^{Image Added} for more details

Gromacs molecular dynamics program.
Installed as root so binaries for MD and the gromacs tools are located in /usr/local/bin/
see website for details: http://www.gromacs.org/^{Image Added}

propka electrostatic and pka computations for proteins.
Usage: see /home/gpw501/software/propka2.0src/README_PROPKA2.0