[gmx-users] Calculate interaction energy dynamically

[Justin Lemkul]

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

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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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