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 ____________________________________________________________________________________ Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
