[gmx-users] Calculate interaction energy dynamically
jalemkul at vt.edu
Mon Jul 22 14:04:27 CEST 2013
On 7/22/13 6:20 AM, Davit Hakobyan wrote:
> Dear Gromacs Users,
> Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script will not help.
> Is there a way to accomplish this?
> One could use the g_select tool to define dynamic groups but again the energy file needs a predefined groups which probably makes the g_select tool useless in this case?
One way that you might approach it is to use mdrun -rerun. You could order the
lipids with respect to the lipid of interest, such that the reference lipid is
always molecule N and the nearest lipid is always written as N+1 in the ordered
trajectory file. Then use normal index groups as your energygrps in the .mdp
file and recalculate the energies with mdrun -rerun.
Justin A. Lemkul, Ph.D.
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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