merc.mertens at gmx.net
Tue Jul 11 15:55:14 CEST 2006
hm, i want to produce one continuous trajectory from several trajectories, that are output from a REMD run. i could not find much information about this matter, but from what i read i gathered that one needs to reorder all the trajectories into a new one using the demux option in trjcat. as far as i understand it, the remd.xvg should contain the information on the replica exchanges to reconstruct their walk through the different trajectories (i.e. the temperature space). but then i might be totally wrong. i have to admit, that somehow i got a bit lost between the concept of a continuous trajectory from REMD simulations and the walk through temperature space of the single replicas. further, i simply do not understand the format of remd.xvg that is shown by trjcat -h. thanks for any help.
-------- Original-Nachricht --------
Datum: Tue, 11 Jul 2006 15:05:04 +0200
Von: Xavier Periole <x.periole at rug.nl>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Betreff: Re: [gmx-users] REMD
> >at the end of a REMD run in gromacs I have as many trajectories as
> replicas used for simulation. To produce one continuous trajectory trjcat was
> recommended in a previous message. Since it neither makes sense to simply
> concatenate all trajectories nor can one sort them by time, I suspect that one
> needs to use the demux option in trjcat. Is that true? And if so, could
> someone explain how this option works, because from the manual I could not
> figure out how the necessary xvg should look like.
> it is not clear what you actually want to do and the trjcat -h
> indicates the format for remd.xvg
> Xavier Periole - Ph.D.
> Dept. of Biophysical Chemistry / MD Group
> Univ. of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Tel: +31-503634329
> Fax: +31-503634398
> email: x.periole at rug.nl
> web-page: http://md.chem.rug.nl/~periole
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