On 12/25/13, 4:55 AM, Asaf Farhi wrote:
Dear all
Hi. We have a question regarding the implementation of free energy calculations
in Gromacs that we have been trying for long time to decipher.
The question is the following:
When transforming molecule A to B if the non bonded interactions are changed
through the topology file e.g:
[ atoms ]
; nr type resnr resid atom cgnr charge mass typeB chargeB massB
1 HC 1 PCH3 H1 1 0.123 1.0080 HC 0.0 1.0080
, will the the interactions of this atom with all the other atoms be affected
by this change of charge?
That depends on how you are setting coupl-intramol (and on a related note, check
out http://redmine.gromacs.org/issues/1340). The nonbonded interactions between
the coupled molecule and its surroundings are affected. Whether or not
intramolecular interactions are affected depends on coupl-intramol.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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