[gmx-users] electrostatic energy calculation
jalemkul at vt.edu
Tue Aug 2 14:02:21 CEST 2016
On 8/2/16 7:53 AM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> That's interesting Alex. mdrun -rerun only works with two energygrps (I
> put more then all g_energy terms come to zero) but you're saying normal
> mdrun works with any number. I don't know if that's intentional or whether
> the developers would like me to make a Redmine..
Sounds like you did your run on GPU, which does not support energygrps.
Post-process with as many groups as you like on CPU only.
>> Hi there,
>> g_energy or gmx energy just lists the short-ranged non-bonded potential
>> energies of those species which have been already indicated in *.mdp file
>> by "energygrps", like energygrps = A B C, then g_energy would offer you
>> something like Coul-SR: A-B , LJ-SR: B-C and so on.
>> On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar <maryam.kowsar at gmail.com>
>>> Dear all,
>>> I want to calculate the electrostatic energy (coulomb SR and LR) for a
>>> of molecules during the whole simulation. I used g_energy -f ener.edr -o
>>> (with or without -nmol option), but it only gives me 1 average output
>>> the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
>>> group.dat file. Is there a way to calculate coulomb energy in all steps
>>> preferably for a set of desired charged molecules?
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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