[gmx-users] Replica exchange MD analysis

[Rituraj Purohit]

Thank you Justin, with your valuable input I got the solution.
regards
RajP

On Mon, Mar 25, 2019 at 11:44 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 3/25/19 2:22 PM, Rituraj Purohit wrote:
> > Thank you Mark for the reply. In my REMD results I would like to
> > observe the structure transition with temperature given variation (I
> > think it is most common observation). My query here is the output of
> > REMD, It does not give .xtc file but only .edr, .log and .gro
> > even-thou I indicated -x .xtc during job submission. Is it possible to
> > perform analysis with .edr, .log & .gro files and without the
> > Trajectory file? If yes, Please let me know how to do different
> > analysis such as RMSD, RMSF, Rg etc..
>
> All of those depend on coordinates over time, i.e. the trajectory. Your
> existing files cannot be used for such analysis. You will only get an
> .xtc file if you specify a non-zero value of nstxout-compressed in the
> .mdp file.
>
> -Justin
>
> > regards
> > RajP
> >
> > On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >> Hi,
> >>
> >> This is the same as for any other scientific experiment. You need to have
> >> thought about what you hope to learn and what you need to record in order
> >> to analyse the results. REMD is essentially no different here.
> >>
> >> Mark
> >>
> >> On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, <riturajpurohit94 at gmail.com>
> >> wrote:
> >>
> >>> Dear Friends,
> >>> I performed REMD by following tutorial provided by Mark Abraham, But I
> >>> am not able to get the analysis part. Is a step-wise tutorial
> >>> available ? I would be thankful to you if anyone of you could help me
> >>> to perform analysis of REMD output. Thanking you
> >>> Regards
> >>> RajP
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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