[gmx-users] Speeding up simulation
sapna.sarupria at gmail.com
Tue Aug 17 23:40:49 CEST 2010
Thanks for your input. I guess I will do some more literature search and try
to optimize the simulations as much as I can.
On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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
>> Thanks for your help.
>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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.
>> Thank you
>> -- ========================================
>> 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
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>> Sapna Sarupria
>> Post-doctoral Researcher
>> Princeton University
>> New Jersey 08540
>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
New Jersey 08540
Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
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