apbs

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. (Summary from the program web page.)

The official web page: http://www.poissonboltzmann.org/apbs

Notes:

The package supports sequential as well as parallel execution via OpenMP, which limits parallel execution to a single computational node. The number of processors is set by OMP_NUM_THREADS variable, which is set automatically by the Infinity environment.

Example script

#!/usr/bin/env infinity-env

module add apbs

apbs input.in

Job submission as a single CPU job

$ psubmit normal test_me          # apbs execution on 1 CPU

Job submission as a parallel job

$ psubmit normal test_me 8        # apbs execution on 8 CPUs