[gmx-users] REMD ensemble of states

[Mark Abraham]

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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