[gmx-users] doubt in remd

[Simone Conti]

Hi!
I'm also working on REMD in these days.
For temperature spacing you can use this web site:
http://folding.bmc.uu.se/remd/
In order to find the most probable structure, which should be the global
minimum, I think you can work with cluster analysis based on rmsd. Or it
can be also useful a secondary structure analysis along the trajectory (if
it is interesting for your system).
If anyone else have some ideas I'm also looking for them.

Simone



2013/4/9 Nikunj Maheshwari <nixcrazyforher at gmail.com>

> Hi. Glad to know that your REMD was successful. We are trying to do the
> same, but are stuck in between.
> Can you tell us, how did you got the temperature spacing?
> Thanks....
>
> On Tue, Apr 9, 2013 at 11:59 AM, Shine A <shine.a at iisertvm.ac.in> wrote:
>
> > Respected sir,
> >
> >                     I successfully  completed REMD simulation. Now I am
> > struggling with analysis part. Here how I select the global minimum  from
> > replica? Can you give some suggestions about the analysis part?
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>