[gmx-users] g_density and g_potential for DMPC bilayer

[Xavier Periole]

>>
>> I don't see where the problem is. You give your trajectory to trjconv
>> trjconv -f traj.xtc -n index.ndx -o trajout.xtc
>> because you specify an index, the program asks you the group you
>> want to center and the group you want as output. So as output you
>> have your whole system centered on the group you choose. The center
>> the program chooses is probably geometrical but check on some snapshots
>> you'll find that it is almost the same as the COM. It would be 
>> necessary
>> to check the code but I am also convinced that the program re-centers
>> in the box at each frame of the trajectory.
>
>
> Well, if trjconv re-centers at each frame, this solves the problem, of 
> course.

you can check with g_traj -f traj.xtc -com -n index.ndx
it'll give you the position of the COM of a chosen group at each frame.