[gmx-users] Problem with trjcat / trjconv

[Michael Patra]

Dear Gromacs users,

I have a problem with reading and writing .trr with trjcat. An identical
problems seems to appear with trjconv. The .trr files were created with version
3.1.3. For trjcat I tried version 3.0.5, 3.1.1, 3.1.3 and 3.1.4, with identical
outcome.

The problem is that the different entries in the header for each frame
get mangled up. The step number seems to get moved into the lambda field,
and the time is copied into the step field.

> gmxdump -f fall111.trr | grep step
[ some lines deleted ]
trn version: GMX_trn_file
   natoms=     30587  step=         0  time=         0  lambda=         0
   natoms=     30587  step=       500  time=         1  lambda=         0
   natoms=     30587  step=      1000  time=         2  lambda=         0
   natoms=     30587  step=      1500  time=         3  lambda=         0
[ many lines deleted ]

> trjcat fall111.trr -o new111.trr
[ some line deleted ]
trn version: GMX_trn_file
Reading frame       0 time    0.000   
[ some lines deleted ]

> gmxdump -f new111.trr | grep step
[ some lines deleted ]
trn version: GMX_trn_file
   natoms=     30587  step=         0  time=         0  lambda=         0
   natoms=     30587  step=         1  time=         1  lambda=       500
   natoms=     30587  step=         2  time=         2  lambda=      1000
   natoms=     30587  step=         3  time=         3  lambda=      1500

Is this a known problem? It should be noted that also other programs (like
tpbconv) work fine on fall111.trr but not on new111.trr, so the problem is not
in gmxdump. The same problem exists with all .trr-files I've tried, also the
ones created by older versions of Gromacs.

Yours faithfully,

- Michael Patra