[edit] APBS on the ITS HPC Cluster

APBS ("Adaptive Poisson-Boltzmann Solver") 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 simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

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.

To run APBS, load the appropriate environment variables using the command

  module load apbs

These changes to the environment remain in effect until logout or the issuance of the command

  module unload apbs

Latest version 1.0.0 is also installed in HPC cluster. To use it, please load following modules.

   module load apbs-1.0

For information on APBS, please see the APBS web site.

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