[gmx-users] g_traj with xtc_grps ... all coordinates zero

Michael Brunsteiner mbx0009 at yahoo.com
Tue Feb 27 03:48:13 CET 2007

Dear all,

In the mdp input file of an MD simulation i have:
nstxtcout                = 20
xtc_grps                 = cwat
I tell mdrun to write the coordinates of a small group 
of 4 waters to a file called traj1.xtc every 20 steps.
the xtc file is created and has a non-zero size.
However, if i say:

g_traj -f traj1.xtc -ox cwat1.xvg -s topol1.tpr

the group of atoms i want to write is not in the
list when g_traj asks me to select a group,
although the group is known to the tpr file
(as i checked with gmxdump).
If i include the index file that contains the group
(and which was also used for the grompp command)
it is in the list, only if i choose it
all the coordinates in the resulting xvg file are zero!

If i look at snapshots of the entire system created by trjconv
from a trr file of the same run this group of molecules is certainly 
there and has non-zero coordinates.

If I make a new tpr file with the same specifications
in the mdp file but with only 4 waters in the input
structure and topology, and use this tpr file with g_traj
it works and the coordinates are fine.

This problem might be due to the fact that I run a parallel
job using openmpi (np=4 on a dual processor/dual core machine
as in:
mpirun -np 4 --hostfile my-hostfile-17 mdrun_mpi -s topol1.tpr \
 -np 4 -o traj1.trr -x traj1.xtc -c confout1.gro -e ener1.edr \
 -g md1.log >& mpirun1.err &   

my gromacs version is 3.3.1, on a linux rocs cluster
with a recent centos version.

a minor issue ... but maybe someone knows how to
make it go away ...


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