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
temperature.
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
3.5,
and so on ... you should concatenate then first then concatenate the
remd.xvg
files (probably by hand) and making sure that the indices in consecutive
remd.xvg files are coherent.
have fun ...
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: [EMAIL PROTECTED]
web-page: http://md.chem.rug.nl/~periole
----------------------------------
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