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 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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