[gmx-users] concaternating remd trajectories using trjcat & demux

Segun Jung dauss75 at gmail.com
Wed Feb 10 16:47:58 CET 2010

Dear gromacs users,

I am trying to collect trajectories corresponding to each temperature by
using trjcat with demux.

There were similar issues posted earlier, but I do not see the solution on
the problem I am facing following:

 I have 64 replicas simulated using namd  in dcd trajectory format and saved
them in gromacs format (.trr) using vmd.

I inspected the gromacs format trajectories by eyes in vmd and looked fine.
However, when I tried trjcat -f g*.trr -demux replica_index.xvg,

the output looked weird. So I tested a small set of the trajectories (using
only replicas 0 to 8 and first two frames) and

noticed that the output does not match to the replica_index.xvg file.

trjcat -f *g*.trr -demux replica_index.xvg


0 0 1 2 3 4 5 7 6

 2 1 0 2 3 5 4 6 7

I am using Ubuntu (32bit) and the gromas version is 4.0.5.

0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from
replica 1, but both frames for 0_trajout.xtc are from the replica 0.

It seems the index file does not cooperate properly with the trjcat and
-demux. Does anyone have clue about this?

 Many thanks,


Segun Jung, Ph.D. Candidate
Computational Biology
Schlick Lab, Department of Chemistry
New York University
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