[gmx-users] Calculate interaction energy dynamically

Justin Lemkul jalemkul at vt.edu
Mon Jul 22 14:39:27 CEST 2013

On 7/22/13 8:37 AM, Davit Hakobyan wrote:
> Thanks very much for all your suggestions!
>> 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.
> Do I understand correctly that in the ordered trajectory each frame should have lipids ordered is such a way that in any two frames N and M the lipids with n and n + 1 indices should be neighbors but these need not necessarily be the same lipids in two frames ?


> Could you also please inform what command may one use to reorder lipids in a trajectory per frame?

Start by reading trjorder -h.  The exact approach depends on what you're dealing 



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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