[gmx-users] center of mass motion

[David van der Spoel]

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.
> 
> Thanks,
> 
> Cherry  
>

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++