On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote:
> Just my 2 cents: REST2 doesn't work. The random walk is much better than > REST but the sampling efficiency at low lambda is now poor. Interesting. Is there any (published) data you could point to that supports this? > Your mileage may vary, but be aware that REST2 is not necessarily going to > be useful for all systems. > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > Piggot <t.pig...@soton.ac.uk> > Sent: 14 April 2017 09:23:35 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Replica exchange simulations more than number of > processor > > In addition, using another technique like REST2 may substantially reduce > the numbers of replica's you need. Still, more compute is definitely > recommended if you can get it. > > Cheers > > Tom > > On 14/04/17 12:48, Smith, Micholas D. wrote: > > You can try over assignment of cores, but that will be horribly slow. Or > use more than 1 node (if you can get it). > > > > =================== > > Micholas Dean Smith, PhD. > > Post-doctoral Research Associate > > University of Tennessee/Oak Ridge National Laboratory > > Center for Molecular Biophysics > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Мижээ > Батсайхан <b.mijidd...@gmail.com> > > Sent: Friday, April 14, 2017 4:16 AM > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Replica exchange simulations more than number of > processor > > > > Dear gmx users, > > > > I would like to simulate folding of a peptides. I have only 12 core > > processor, and I assumed the number of replica using temperature > generator > > as following link > > http://folding.bmc.uu.se/remd/. > > > > The number of replica is about 60. How can I solve this problem? Can you > > advice me, please? > > > > Best regards, > > Mijee > > -- > > 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. > > > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > -- > 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. > -- 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.
