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

Justin Lemkul jalemkul at vt.edu
Sat Nov 21 00:46:51 CET 2015

On 11/20/15 2:53 PM, S.M. Golam Mortuza wrote:
> 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.

AFAIK, there is no such feature.  This would require calculation of COM 
positions of desired group(s) every time write_traj() is called, which impairs 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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