[gmx-users] Zero LJ energies during Free energy perturbation

Justin Lemkul jalemkul at vt.edu
Fri Feb 7 22:43:43 CET 2014

On 2/7/14, 9:13 AM, bipin singh wrote:
> Hello All,
> Using a B state topology in mdp file, I have switched off the vdw and
> coulombic terms of a single atom in a molecule (H atom in CH3OH). I have
> tried to see how the LJ energies (between CH3OH and solvent) changes during
> the transformation (from lambda=0 to lambda=1) but I get zero values at
> both the lambda point (0 and 1) for both the LJ-SR and LJ-14 terms for
> CH3OH and solvent LJ interaction.

H atoms do not have LJ parameters in most force fields, so you will not see any 
changes.  LJ-14 are intramolecular and those interactions are going to all be 
excluded anyway in CH3OH, but again if an H is changing, there will be no 
difference in LJ energy.



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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