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APBS (Adaptive Poisson-Boltzmann Solver) on Biowulf

APBS is a software package for the numerical 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. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

Setting up an APBS batch job

Create a batch input file, e.g. 'apbs_run', which uses the input file ''. For example:

#PBS -N apbs
#PBS -e apbs.err
#PBS -o apbs.log

module load apbs
apbs < > apbs.out

Submit this job using the PBS 'qsub' command.

qsub -l nodes=1 myscript

See here for more information about PBS. Example input files and expected output can be found in the directory /usr/local/apbs/share/examples.

See here for more information about using environment variables.


Input files are available in /usr/local/apbs/share/examples.