[gmx-users] REMD ensemble of states

[Abramyan, Tigran]

Thank you Mark,

One more question regarding the centering of the frames at 300 replica (0.xtc) using trjconv. I have used a few trjconv options, however do not seem to be removing jumps from the original trajectory. For example, the command below works for me when applied to the *xtc file produced in regular MD, however, with REMD it produces a trajectory which won't be of use for example in VMD:

 echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40

I am assuming I may need to use a combination of tpr files to produce the nojump 300.xtc file?

Please advise,
Thank you very much.
Tigran


________________________________________
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 1:15 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states

Yes

On Tue, 8 Nov 2016 18:43 Abramyan, Tigran <tigran at 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-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
>
> Hi,
>
> Mdrun wrote that. You made the trajectories contiguous with the demux.
>
> Mark
>
> On Tue, 8 Nov 2016 04:55 Abramyan, Tigran <tigran at 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
> >
> > --
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