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
performance.
-Justin
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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