Yes On Tue, 8 Nov 2016 18:43 Abramyan, Tigran <tig...@email.unc.edu> wrote:
> Hi Mark, > > Thanks a lot for your prompt response. So demux.pl creates continuous > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > ensemble, typically of interest in the analysis of REMD results) is saved > in the original 0.xtc file produced during REMD before using demux.pl? > > Thank you, > Tigran > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham <mark.j.abra...@gmail.com> > Sent: Tuesday, November 8, 2016 5:53 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Hi, > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > Mark > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran <tig...@email.unc.edu> wrote: > > > Hi, > > > > > > I conducted REMD, and extracted the trajectories via > > trjcat -f *.trr -demux replica_index.xvg > > And now I was wondering which *.xtc file is the ensemble of states at the > > baseline replica (lowest temperature replica). Intuitively my guess is > that > > the numbers in the names of *_trajout.xtc files correspond to the replica > > numbers starting from the baseline, and hence 0_trajout.xtc is the > ensemble > > of states at the baseline replica, but I may be wrong. > > > > > > Please suggest. > > > > > > Thank you, > > > > Tigran > > > > > > -- > > Tigran M. Abramyan, Ph.D. > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > Center for Integrative Chemical Biology and Drug Discovery > > Eshelman School of Pharmacy > > University of North Carolina at Chapel Hill > > Chapel Hill, NC 27599-7363 > > > > -- > > 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.