[gmx-users] About running Production simulation in GPU with twinrange cut-off
jalemkul at vt.edu
Sun Aug 11 13:52:19 CEST 2013
On 8/11/13 3:02 AM, vidhya sankar wrote:
> Thank you Justin
> To check Performance in GPU i Need to run simulation with same parameters for r coulomb = rvdw
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.4
> But i need to use twin range interaction with rvdw = 1.4; r coulomb = 0.9 in GPU
> May i use different option -nb or -tunepme option of mdrun
> instead -testverlet
mdrun -nb gpu should be sufficient to run on the GPU. The -tunepme option is
> But in one mail to me you said that the defaut parameters for Gromos96 53A6,
> nstlist = 5
> rlist = 0.9
> rcoulomb = 0.9
> rvdw = 1.4
> but if i run on GPU regularly i need to change rcoulomb = 1.4 from 0.9 Will it Affect the result ?
> or is it reasonable to change ?
When using PME, the value of rcoulomb is a bit more flexible than other
settings, but you need to carefully validate that such modifications do not
invalidate the proper use of the force field. As previous threads have very
clearly demonstrated, the increase in speed is irrelevant if the results are
influenced by artifacts.
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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