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
not relevant.
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
--
==================================================
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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