[gmx-users] REMD analysis of trajectories

[Mark Abraham]

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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