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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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