merc mertens wrote:
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
have you run
gmxcheck -f file.trr ?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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