[gmx-users] center of mass motion
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 17 07:46:43 CET 2007
Cherry Y. Yates wrote:
> 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.
If there are no interactions they should continue going, but it could
also be a side effect of other things. Pressure coupling, shake/lincs etc.
Please provide more details.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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