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

From: David A Case <>
Date: Mon, 4 Jun 2018 14:21:56 -0500

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 - 12:30:02 PDT
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