Thanks for the paper, I will look at it! Cheers Jianguo
On Thursday, 12 December 2013, 18:54, Thomas Evangelidis <teva...@gmail.com> wrote: I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a quite flexible implementation of Hamiltonian REMD for GROMACS. It may be worth-checking it: http://arxiv.org/abs/1307.5144 On 12 December 2013 12:11, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Quite right, sorry. P as the control variable is not implemented. NPT with > T as the control variable is, for example. > > Mark > > > On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts <mrshi...@gmail.com> > wrote: > > > Pressure replica exchange is not in currently. It will be added > > eventually (it's not that hard, just takes time, and hasn't been a > > priority.). > > > > Note that pressure temperature control with berendsen pressure control > > will be 100% wrong. For pressure replica exchange to work, the > > barostat has to give the correct volume fluctuations, and berendsen > > does not give correct volume fluctuations. > > > > Of course, that's irrelevant since pressure replica exchange isn't in > yet. > > > > The exchange criteria is always of the form min(1,exp(-X), where X = > > \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can > > vary with state. > > > > What is in is temperature replica exchange with NPT, where beta > > changes, but P stays the same. > > > > On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li <ljg...@yahoo.com.sg> wrote: > > > Thanks very much. As you suggested, making T with small increments such > > as 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > > > > > I am trying to do replica exchange at different surface tensions for my > > membrane system. > > > To achieve different surface tensions for different replica, I only > > changed Pxy, but keep Pz the same for all replica. > > > pcoupl = berendsen > > > pcoupltype = semi-isotropic > > > tau_p = 0.5 0.5 > > > ref_p = 1.0 1.0 ; Pxy and Pz > > > compressibility = 4.5e-5 4.5e-5 > > > > > > I noticed that in the manual, the eq (3.141) shows the exchange > > probability. Can you explain what does the P1 and P2 represent? Pxy or > Pz? > > > > > > Also, the manual mentioned about using Hamiltonian and temperature > > replica exchange simultaneously (eq 3.143). But there is no pressure term > > in the acceptance criteria (eq 3.143). I am wondering if > > pressure+temperature+Hamiltonian replica exchange has been implemented in > > Gromacs. If yes, what is the general equation of acceptance criteria? > > > > > > Cheers, > > > Jianguo > > > > > > > > > > > > > > > > > > > > > > > > On Tuesday, 10 December 2013, 17:49, Mark Abraham < > > mark.j.abra...@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li <ljg...@yahoo.com.sg> > wrote: > > > > > > Dear All, > > >> > > >>Is it possible to do pressure based replica exchange simulations in > > gromacs? Basically I want to do replica exchange simulations for my > > membrane system at different surface tensions. If I just set different > > pressures in the mpd file, then the mdrun will complain "systems are all > > the same, there is nothing to exchange". Is there any other parameters I > > need to set? > > >> > > > > > > Yes, the implementation is a bit broken, and requires that one of ref-t > > or lambda varies before it even considers the pressure. If you want T > > constant and P as the replica control variable, you can can only do that > by > > fooling the implementation by having T vary in tiny increments. > > > > > > Mark > > > > > > > > >>Thanks a lot! > > >> > > >>Jianguo > > >>-- > > >>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. > > > -- > 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. > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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.