merc mertens wrote:
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).
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.
________________________________________________________________________
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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