[gmx-users] REMD

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
>> -- 
>> ----------------------------------
>>  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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