[gmx-users] g_msd in combination with -mol -commm

[Alberto Duepietre]

Dear Gromacs Users,

I am using g_msd to calculate the lateral msd of the center of mass  of a
lipid molecule in a membrane. When I run the command:

g_msd -f traj.xtc -s topol.tpr -n index.ndx -o lipid_lmsd.xvg -mol -lateral
z

I got the correct results.
Now, I would like to remove the center of mass of the whole membrane before
calculating the msd. According to  the manual the option -rmcomm does the
job.
However, when I run:

g_msd -f traj.xtc -s topol.tpr -n index.ndx -o lipid_lmsd.xvg -mol -lateral
z -rmcomm

g_msd get stuck at the first frame:

…
Split group of 138 atoms into 1 molecules
Reading frame       0 time 15475.000

Note that the -rmcomm option works properly if I use it without the -mol
one, i.e. without requiring the msd of the center of mass of the lipid
molecule:

g_msd -f traj.xtc -s topol.tpr -n index.ndx -o lipid_lmsd.xvg -lateral z
-rmcomm

I tried with g_msd in the gromacs 4.5.5 and 4.6.3 packages with the same
result.

Is this a problem of g_msd or am I missing something?

Best regards,
Alberto