[gmx-users] Maximal nrexcl
jalemkul at vt.edu
Tue Jan 21 04:40:29 CET 2014
On 1/20/14, 8:17 PM, cynthiahong1983 wrote:
> Dear All,
> Does anyone know whether there is a maximal limit for nrexcl?
> I tried to calculate the intermolecular energy between polymeric molecules through "mdrun -rerun" and a large "nrexcl". But when the molecule becomes very long e.g. having ~ 20 bonds in the backbone and I set nrexcl = 20 , grompp beccame very slowly and just terminated in error like "4210 terminated" (the number changed each time when it failed.)
> Someone ever met with similar situations?
The only real limitation is available memory. For this case, you'd need a lot
of it. The other option (depending on how many polymers you have) would be to
assign each one to individual energygrps in the .mdp and .ndx files.
Justin A. Lemkul, Ph.D.
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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