[gmx-users] REMD

[merc mertens]

> > the "time" stamps correspond to the first column in remd.xvg used for
> trjcat. further, if *xtc is chosen as output in trjcat, for every single
> frame the *xtc file contains the line: "not available: x", where there surely
> is x in the single *trr files!
> > 
> > e.g.: gmxdump_d -f traj0.trr
> > 
> > traj0.trr frame 0:
> >    natoms=     14670  step=         0  time=         0  lambda=        
> 0
> >    box (3x3):
> >       box[    0]={ 8.48915e+00,  0.00000e+00,  0.00000e+00}
> >       box[    1]={ 0.00000e+00,  4.99054e+00,  0.00000e+00}
> >       box[    2]={ 0.00000e+00,  0.00000e+00,  3.49561e+00}
> >    x (14670x3):
> >       x[    0]={ 1.98230e+00,  2.07120e+00,  3.06491e+00}
> >       x[    1]={ 1.93097e+00,  2.10502e+00,  3.14505e+00}
> >       x[    2]={ 1.92314e+00,  2.07599e+00,  2.98319e+00}
> > ...
> > 
> > for sure i am doing something wrong here, i just do not get what.
> > i am puzzled, thanks for any help, merc
> > 
> have you run
> gmxcheck -f file.trr ?
> 
> -- 
> David.

gmxcheck tells me for every single trajectory:

Item        #frames Timestep (ps)
Step          2001    1
Time          2001    1
Lambda        2001    1
Coords        2001    1
Velocities      21    100
Forces          21    100
Box           2001    1

so, the timestep (for the coordinates) is correct in the xvg and the first and last lines in the xvg are:

 0 0 1 2 3 4 5 6 7 8 9 10 11
...
 2000 0 1 2 3 4 5 6 7 8 9 10 11

and that should be okay as well, i think. can the problems be related to using the wrong format for remd.xvg(e.g. trailing spaces, missing tabs)?
btw.  i understood, that one should get back as many trajectories as were input to trjcat. nevertheless using something like:

trjcat -f traj0.trr traj1.trr ... traj11.trr -o j0.xtc j1.xtc ... j11.xtc -demux remd.xvg

outputs always only one trajectory.
-- 


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