[gmx-users] REMD

[merc mertens]

> > 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).
> How about the trr files? Are they written with the same frequency as 
> what you have in the remd.xvg file? Otherwise I don't know what will 
> happen...
> 
> -- 
> David.

when trying:  gmxdump -f traj0.trr | grep time

sample output is:
   natoms=     14670  step=         0  time=         0  lambda=         0
   natoms=     14670  step=       500  time=         1  lambda=         0
   natoms=     14670  step=      1000  time=         2  lambda=         0
   natoms=     14670  step=      1500  time=         3  lambda=         0
   natoms=     14670  step=      2000  time=         4  lambda=         0
   natoms=     14670  step=      2500  time=         5  lambda=         0
...

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

-- 


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