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 ?
Yes.
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
with.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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