sapna sarupria wrote:
Hi Justin
Thanks for your response. I suspect that it is the same thing. Is there
a way to make gromacs use PME only within a certain region of the
simulation box? Also, how does one know how to fix the load imbalances
(in this context)?
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. 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.
Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
--
========================================
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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