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.
-Justin
Thank you
Sincerely
Sapna
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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