[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

[NISHA Prakash]

Hi Mark,

All I want to know is the first step that I have to take in analyzing the
trajectories. By way of mentioning what I want to do was to essentially
list out my aim only to make my question clear.
With REMD results, I want to know whether analyzing individual ensemble is
the way to go or look at the ensembles together, this is because I would
like to bring out a comparison between the simulations with protein bound
to three different ligands.

I hope I have made myself clear.

Thanks again,

Nisha



On Fri, Apr 3, 2015 at 9:33 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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