David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 11 16:00:41 CEST 2006
On Tue, 11 Jul 2006, merc mertens wrote:
>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.
you do need this option (-demux) and the xvg file should hold N+1 columns
containing the correct permutation of replicas, e.g.
time repl 0 1 2 3 ...
0 0 1 2 3
1 1 0 2 3
2 1 2 0 3
and so on
>-------- 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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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://xray.bmc.uu.se/~spoel
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