Solvent Boundary Potential Utilizer
The solvent Boundary Potential Utilizer helps you to generate a series of CHARMM inputs to
perform MD simulations with three types of solvent boundary potentials in CHARMM;
-
SBound (sbound.doc)
SBound uses the deformable (stochastic) solvent boundary potential to study a small region of interest (such as an active site) in biomacromolecules. The boundary forces are applied to the atoms in the solvent and serve to contain the reaction zone. -
SSBP (mmfp.doc)
SSBP stands for Spherical Solvent Boundary Potential and the SSBP potential corresponds to a constant temperature and constant pressure system. SSBP contains several contributions from the external pressure and surface tension, the mean solute-solvent van der Waals interactions (similar to SBound), the reaction field due to a dielectric continuum surrounding a cavity containing a charge distribution, and an angular correction to restore the isotropic angular distribution near the edge of the sphere. -
GSBP (pbeq.doc)
GSBP stands for Generalized Solvent Boundary Potential. The system is partitioned in two regions: an inner region of interest and an outer region. The inner region includes all atom explicitly. GSBP represents the electrostatic forces from the outer region as the sum of two components. One is the static external field which arises from the charge distribution in the outer region (taking into consideration the solvent as a featureless dielectric medium). The second contribution is the reaction field which is created by the charge distribution inside the inner region considering the whole molecular configuration and the dielectric solvent.
- one of the boundary potential methods and its options
- size and position of a spherical region of interest
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