[gmx-users] question regarding free energy calculations

Justin Lemkul jalemkul at vt.edu
Thu Dec 26 14:08:46 CET 2013

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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