[gmx-users] REMD ensemble of states

[Abramyan, Tigran]

Hi Mark,

I understand that at each replica the coordinates of the accepted states are saved. I understand that I can calculate different properties of 0.xtc in differenr programs, e.g., gromacs, MDTraj, etc., but when it comes down to visualization in VMD, for example, in gromacs I don't seem to find a way to remove the jumps and superpose the coordinates saved in 0.xtc.

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: Monday, November 14, 2016 1:20 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states

Hi,

The ensemble at each temperature is intrinsically discontinuous. You can't
make it look continuous. What are you trying to do?

Mark

On Mon, 14 Nov 2016 05:26 Abramyan, Tigran <tigran at email.unc.edu> wrote:

> 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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