Re: [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-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: Monday, November 14, 2016 1:20 AM
To: gmx-us...@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 <tig...@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-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 1:15 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REMD ensemble of states
>
> 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

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

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
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>
> * Please search the archive at
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> posting!
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Re: [gmx-users] REMD ensemble of states

[Mark Abraham]

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
>
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>
> * Please search the archive at
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Re: [gmx-users] REMD ensemble of states

[Abramyan, Tigran]

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.
>
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Re: [gmx-users] REMD ensemble of states

[Mark Abraham]

Hi,

Mdrun wrote that. You made the trajectories contiguous with the demux.

Mark

On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  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.
>
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