[gmx-users] Dumping centers of mass of molecules during MD simulation

S.M. Golam Mortuza mortuza862 at yahoo.com
Fri Nov 20 20:53:32 CET 2015

Dear Gromacs User,
Instead of dumping all atoms of a specific type of molecules, I would like to dump centers of mass (COM) of the molecules during MD simulations in Gromacs to reduce trajectory storage. I know g_traj can be used to dump COM of molecules from trajectory files. But, in that case, I've to generate the trajectory file first, and, that's storage consuming, since it has information of all atoms. Also, I know that xtc_grps in .mdp file dumps specific group of atoms/molecules and create traj.xtc. I am just wondering if there is any command that I can use in .mdp file to dump COM of the specific groups mentioned in xtc_grps. I would really appreciate if anyone can help me in this regard.
Thanks in advance for  your valuable time.


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