[gmx-users] REMD

[merc mertens]

> >
> >so, if i observe in md.log an exchange like:
> >"Repl ex  0    1    2 x   3" for e.g. time step 1
> >that would convert into:
> >"1      0   1   3   2"
> >for remd.xvg. is that correct?
> >the problem is, if i do something like this for the entire time scale
> trjcat only outputs the simulation box but no coordinates to the new
> trajectory. 
> >
> 
> details please.
> do you give trjcat N trajectories? then you should get N back as well.
> give your entire command line and a snippet from the xvg file.

this is what i did (using gromacs 3.3.1):

trjcat -f traj*.trr -o j.trr -demux remd.xvg

trjcat reads:
traj0.trr, traj1.trr - traj11.trr

and remd.xvg contains lines like:
 0 0 1 2 3 4 5 6 7 8 9 10 11
 1 0 1 2 3 5 4 6 7 8 9 11 10     
 2 0 1 2 3 4 5 6 8 7 10 9 11     
 3 0 1 2 3 4 5 6 7 8 9 10 11     
 4 0 1 2 3 4 5 6 7 8 9 10 11     
 5 0 1 2 3 4 5 6 7 8 9 10 11     
 6 0 1 2 3 4 5 6 7 8 9 10 11     
 7 0 1 2 3 4 5 7 6 8 9 10 11     
 8 0 1 2 3 4 5 6 7 8 9 10 11     
 9 0 1 3 2 4 5 6 7 8 9 10 11     

remd.xvg was build like described above. output is only one trajectory, containing only box information.

additionally i tried:

trjcat -f traj0.trr traj1.trr traj2.trr ... -o j0.xtc j1.xtc j2.xtc ... -demux remd.xvg

but from that i got only one trajectory as output, too (also only containing box info).
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