[gmx-users] Calculate interaction energy dynamically

[Justin Lemkul]

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
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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