Re: [AMBER] Query regarding 3D-RISM output

From: Rakesh Srivastava <>
Date: Tue, 5 Jun 2018 10:21:02 +0530

Thanks dac,
Your reply really cleared my doubts.

Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067

On Tue, Jun 5, 2018 at 12:51 AM, David A Case <>

> On Mon, Jun 04, 2018, Rakesh Srivastava wrote:
> >
> > Please let me know, what exactly
> > *rism_totalParticles, rism_totalCharge, rism_excessParticles* and
> > *rism_excessCharge* values in 3D-RISM output file represent as these are
> > not much explained in manual. Further kindly tell whether these values
> also
> > depend on buffer distance (in other words, box volume) taken for 3D-RISM
> > calculation or not.
> totalParticles gives the total number of particles (for each solvent
> atom type) in box surrounding your solute. totalCharge is the
> total charge of each solvent type in the box (plus a total entry.)
> excessParticles and excessCharge give the difference between the actual
> values (with the solute present), and what one would have in the same
> box with just solvent (and no solute). The excessCharge is broken in to
> entries just on the grid points in the box, and a total amount that
> includes a contribution of the excess charge that is outside the box.
> For non-periodic simulations, the excessCharge (including the long-range
> correction) should be equal to the negative of the solute net charge.
> All of these indeed depend on the box volume. The excess quantitites
> should converge to limiting values as the box gets bigger and bigger.
> ....hope this helps....dac
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Received on Mon Jun 04 2018 - 22:00:02 PDT
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