Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters*<http://www.sciencedirect.com/science/journal/00092614> Volume 406, Issues 1-3<http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%235231%232005%23995939998%23591997%23FLA%23&_cdi=5231&_pubType=J&view=c&_auth=y&_acct=C000062818&_version=1&_urlVersion=0&_userid=6325866&md5=51f91ba17c3ce282da206786a17d50d5>, 23 April 2005, Pages 49-53
-Gaurav On Wed, Aug 18, 2010 at 12:04 PM, sapna sarupria <[email protected]>wrote: > That might actually be the best approach speed wise. But it depends on what > level of accuracy you wish for your calculations. What is your system like? > May be you can have a large cut off but you will have to see what the trade > off between speed and accuracy is. > > > On Wed, Aug 18, 2010 at 10:26 AM, ms <[email protected]> wrote: > >> 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 >>>> >>>> ======================================== >>>> -- 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 >>>> >>>> >>> >> -- >> 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 >
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