Re: [gmx-users] Since nstlist has no effect on the accuracy
Exactly. The penalty of large nstlist is large buffer (rlist), but up to 40-50 with CPUs and up to 100 with GPUs is quite realistic. Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in the mdp. From 5.0 there will be a command line option. Cheers, -- Szilárd On Thu, Feb 6, 2014 at 2:29 AM, yunshi11 . yunsh...@gmail.com wrote: In a MD run with Verlet cutoff scheme, can I set nstlist as large as possible? Like 100 or 1000? Thanks, Yun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Since nstlist has no effect on the accuracy
PS: The buffer is automatically calculated based on the verlet-buffer-drift set in the mdp file, for more details see the appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003. -- Szilárd On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll pall.szil...@gmail.com wrote: Exactly. The penalty of large nstlist is large buffer (rlist), but up to 40-50 with CPUs and up to 100 with GPUs is quite realistic. Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in the mdp. From 5.0 there will be a command line option. Cheers, -- Szilárd On Thu, Feb 6, 2014 at 2:29 AM, yunshi11 . yunsh...@gmail.com wrote: In a MD run with Verlet cutoff scheme, can I set nstlist as large as possible? Like 100 or 1000? Thanks, Yun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Since nstlist has no effect on the accuracy
Preso appuntamento per sabato mattina...di al papa' che si tenga libero!!! Ivan On 02/06/2014 11:09 AM, Szilárd Páll wrote: PS: The buffer is automatically calculated based on the verlet-buffer-drift set in the mdp file, for more details see the appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003. -- Szilárd On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll pall.szil...@gmail.com wrote: Exactly. The penalty of large nstlist is large buffer (rlist), but up to 40-50 with CPUs and up to 100 with GPUs is quite realistic. Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in the mdp. From 5.0 there will be a command line option. Cheers, -- Szilárd On Thu, Feb 6, 2014 at 2:29 AM, yunshi11 . yunsh...@gmail.com wrote: In a MD run with Verlet cutoff scheme, can I set nstlist as large as possible? Like 100 or 1000? Thanks, Yun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail: iglad...@sissa.it web page: http://people.sissa.it/~igladich/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
