[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

[Mark Abraham]

Hi,

You seem to be essentially asking for your experiment to be designed for
you, after an arbitrary simulation is complete. You should think about what
and how to observe before you simulate, e.g. from what others have done for
similar systems.

Consideration of reweighting is secondary. Generally, the only difference
with REMD simulations is that you cannot assume that the set of frames from
an ensemble are from a contiguous trajectory.

Mark
On 03/04/2015 11:21 am, "NISHA Prakash" <nishnith20591 at gmail.com> wrote:

> 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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