[gmx-users] Speeding up simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 17 23:29:38 CEST 2010

sapna sarupria wrote:
> Hi all,
> I am running (NVT) simulations of a drop of water (~5 nm in radius) in a 
> big box (~25 nm) in a box and find that the simulations are rather slow. 
> I am getting about 0.8 ns per day when a simulation of bulk system of 
> equivalent number of waters will be much faster. The number of waters is 
> ~12000. I was wondering if anyone can suggest methods with which I can 
> speed up the simulations. I am using domain decomposition and 
> optimize_fft is set to yes. PME is used for the electrostatics.

I would suspect that the lag comes from a lot of unused PME calculations. 
During your run, PME grid points will be assigned to vacuum space, for which 
nothing needs to be done.  You can check imbalances and performance loss in the 
log file.


> Thank you
> Sincerely
> Sapna


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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