[gmx-users] REMD analysis of trajectories

[Smith, Micholas D.]

Ouyang,

Each Replica corresponds to 1 temperature in Gromacs (unlike other software packages). If you want to have continuous trajectories (i.e. follow the motion of one replica through temperature exchanges) then you have to demux. But the demux is really only useful (in my experience) with use of the retired g_kinetics tool.


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
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: Thursday, June 01, 2017 10:53 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] REMD analysis of trajectories

Hi,

What did you learn from the first sentence of the link I gave you?

Mark

On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283893 at 163.com> wrote:

> Do you mean  that the original trajectories REMD generated are belong to
> "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?
>
>
>
> Ouyang
>
>
>
>
> At 2017-06-01 21:00:52, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >Hi,
> >
> >That's what you already have. See
> >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
> >
> >Mark
> >
> >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283893 at 163.com> wrote:
> >
> >> Hi,
> >>    I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
> >> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory
> at
> >> specific temperature  such as a trajectory at experiment temperature
> 298K
> >> rather than analyzing the continuous trajectory. I have known GROMACS
> >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
> >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need
> to
> >> do something else on the trajectories to get a trajectory at specific
> >> temperature(i.e. 298K)?
> >>
> >> Best regards,
> >> Ouyang
> >> --
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