[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

[Mark Abraham]

On Tue, Mar 24, 2015 at 6:57 PM, NISHA Prakash <nishnith20591 at gmail.com>
wrote:

> Dear all,
>
> I have simulated the protein ligand complex at 18 different temperatures. I
> was wondering if it was right to concatenate the trajectories of 18
> replicas because they are at different temperatures, with different initial
> structures but have the same start time.
>

It's nonsense to simply combine observations made in different ensembles
(unless using a reweighting scheme).

Use of -demux flag is resulting in independent .xtc files instead of one
> continuous trajectory file.
>
> Use of -cat is giving a WARNING: same Start time as previous.
>
> How do I get a single continuous trajectory for analysis or should the
> trajectories from each of the replica be analysed separately?
>

You have 18 continuous trajectories in different ensembles, or 18 ensembles
with discontinuities. What you want to do depends on what you want to
observe, which you knew before you did the simulation, right? ;-)

I am new to REMD so any help with respect to analysis in the form of
> tutorial will be highly appreciated.
>

Google knows well what there is, e.g.
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B
which describes some uses of demux.

Mark


> Awaiting response.
>
> Thanks!
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