Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can.
Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul <[email protected]> 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 >> 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 >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
