[AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential

From: Brian Radak <radak004.umn.edu>
Date: Thu, 26 Jun 2014 17:06:16 -0400

I'm looking to do simple comparisons of 3D-RISM and NLPB calculations of a
large biomolecule in solvent. Although solute-solvent pair distribution
functions are natural outputs of both types of calculations, rism3d.snglpnt
does not seem to readily output the total electrostatic potential (although
presumably it *must* calculate this at some point, even if it includes
contributions from Lennard-Jones terms).

I suppose my question is this: how can I calculate the electrostatic
potential on the 3D-RISM grid? Presumably there is some relation (although
perhaps not at all trivial) to the charge density (--quv) and/or charge
distribution (--chgdist), but the manual does not seem to indicate what
these quantities actually are (are they related to the solvent site PDFs?
do they include solute contributions in seem charge smearing manner?) How
are the charge density and charge distribution different? If they are
trivially different by a factor of one over the cell size, that seems like
a somewhat frivolous output...


================================ Current Address =======================
 Brian Radak                                            :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities          :     Center for
Integrative Proteomics Room 308
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 Department of Chemistry                          :     Piscataway, NJ
 radak004.umn.edu                                 :
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Received on Thu Jun 26 2014 - 14:30:02 PDT
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