[gmx-users] REMD

Xavier Periole x.periole at rug.nl
Tue Jul 11 16:32:40 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.
If I understand you want to be able to follow a replica through the 
This seems easy with the trjcat -demux. look at it again it is just time 
and then
the indice of the replica.

>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
This file should be generated by the run no !!? I run REMD on gmx3.1 so 
it is
a bit different, but this file is definitely necessary.

Then if you actually have several REMD simulations, eg. 0 to 2ns, 2ns to 
and so on ... you should concatenate then first then concatenate the 
files (probably by hand) and making sure that the indices in consecutive
remd.xvg files are coherent.

have fun ...

 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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