[gmx-users] center of mass motion

Cherry Y. Yates yappik4050 at yahoo.com
Wed Jan 17 02:57:02 CET 2007

Dear Gromacs users and developers,

I am studying a system consisting of six molecules (3 groups). I would like to
keep the center-of-mass motion of each molecule with the system having zero
center-of-mass motion. So I set comm_mode=Linear. In the simulation,
immediately the center-of-mass motion of the system was adjusted to zero;
however, the center-of-mass motion of each group decreases monotonically also,
and after ~100ps, all the center-of-mass motion of each group is zero. I wonder
how it could happen. The distances between molecules are bigger than 1nm, and I
set the cut-offs of Columb and L-J are both 1nm, so there are basically no
inter-molecule interaction unless they colide with each other. But I found the
center-of-mass motion goes to zero before any collision happens.



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