[gmx-users] Replica Exchange Analysis Tools

[Robert Johnson]

I'm getting an error message when feeding replica_index.xvg to trjcat.
Here is the command and the error message:

trjcat -f *.xtc -demux replica_index.xvg


Program trjcat, VERSION 3.3.99_development_20060330
Source code file: gmx_trjcat.c, line: 296

Fatal error:
Demuxing the same replica 1 twice at time 2.400000


Here, the xtc files are the trajectories of only the single stranded
DNA (which is just a subset of my system and is the whole reason why
I'm doing REMD) - not sure if that matters or not. Also, I saved the
ssDNA coordinates at the same frequency as my REMD swaps - one every
0.6 ps. There were 64 replicas total and each replica was running on
32 processors.

Also, what will trjcat give me? Will it give trajectories that are at
a constant temperature?
Thanks,
Bob

On 1/16/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Robert Johnson wrote:
> > Hello everyone,
> > I'm using the current development version of Gromacs to perform
> > replica exchange MD. Are there any Gromacs tools to aid in the
> > analysis of the trajectories. For example, are there tools that enable
> > trajectories grouped by temperature? Is there a way to determine the
> > temperature of a replica as a function of time?
> > Thanks,
> > Bob Johnson
> > PhD Student
> > University of Pennsylvania
> > _______________________________________________
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> There is a script in src/contrib/scripts/demux.pl that will give you
> this info. Please check and double check. It also gives input to trjcat
> for demultiplexing trajectories. If you really are using the development
> version, then do a cvs update, I just added a feature today.
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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