Sapna, Is there a particular reason you're using a box so much larger than the droplet diameter? If your only concern is that periodic images should not see each-other maybe you can use a box length=droplet diameter+2*largest cut-off in the system.
Also using a more spherical box shape such as rhombic dodecahedron or the truncated octahedron will help you in reducing the volume of unfilled space. -Gaurav On Tue, Aug 17, 2010 at 5:40 PM, sapna sarupria <sapna.sarup...@gmail.com>wrote: > 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 <jalem...@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 >>> 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 <jalem...@vt.edu<mailto: >>> jalem...@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. >>> >>> -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 gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> 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 gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php