On 17/08/10 22:36, Justin A. Lemkul wrote:
There is no way to limit PME to certain ranges. It is a method for
solving infinite sums. Usually PME is a poor choice for in vacuo
simulations and the like, since there's nothing to be done for most of
the simulation box.
This interests me -I've used simple cut-off for in vacuo tests, but I
still hadn't made my mind on what electrostatic model I should truly
use. Do you have any suggestion?
thanks,
M.
You may want to see how others (in the literature)
deal with droplet-type simulations.
-Justin
Thanks for your help.
Sapna
On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.
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