[gmx-users] REMD ensemble of states
tigran at email.unc.edu
Tue Nov 8 18:43:23 CET 2016
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?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Tuesday, November 8, 2016 5:53 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states
Mdrun wrote that. You made the trajectories contiguous with the demux.
On Tue, 8 Nov 2016 04:55 Abramyan, Tigran <tigran at email.unc.edu> wrote:
> 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 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
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