[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

[NISHA Prakash]

Hi Mark,

Thanks for your quick response.
Can you please suggest a way out?
As you pointed out previously, I have 18 ensembles and I would like to
study the conformational changes, the interactions between the protein and
the ligand and finally, I would like to extract the stable conformation
from the simulation data.
How do I go about analysing the REMD results.
Your tutorial was indeed very helpful but apart from that, I couldn't find
much information in that area.

Thanks again,
Nisha

On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> There's nothing in GROMACS that specifically supports reweighting
> replica-exchange simulations.
>
> Mark
> On 03/04/2015 10:03 am, "NISHA Prakash" <nishnith20591 at gmail.com> wrote:
>
> > Hi,
> >
> > Can somebody please help with WHAM reweighting scheme for REMD analysis.
> > The command "gmx wham" works for Umbrella sampling simulation but I
> couldnt
> > find a way out for T-REMD.
> > There are similar questions which have been posted here but
> unfortunately,
> > I haven't found answers for the same.
> > WHAM for REMD has been well documented for AMBER but I couldnt find any
> > help for Gromacs.
> > I am a novice in the field and help is appreciated.
> >
> > Thanks!
> >
> > Nisha
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