When I stopCM of the whole system, all running is ok, but I found the infinite surface oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. Then I stopCM of the surface only, I get a lot of warnings about the Large VCM(group rest) (group rest = SOL in my system). Thanks for your attention.
> Stop COM of the whole system? > > > > 2008/4/6 Bo Zhou <[EMAIL PROTECTED]>: > > > Dear gmx users, > > > > My previous question are: > > > > >I want to simulate the solid/liquid interface, so I build an infinite > > inorganic molecule with pbc=full first. After I ran the system > > > with vaccum (at the top of system) for a few ps, I found the crystal > > oscillating along the xy plane collectively and frequently, > > > so there were too much inconsistent shifts. I wonder if it is > > reasonable, > > if not, is there any solution for it? Any suggestions > > > would be helpful. Thanks. > > > > I have tested one system with infinite crystal only, and it turns out be > > to > > quite stable (no collective motion has been found), but when I put some > > water molecules on it, the crystal surface turns out to be what I have > > said > > above. Then I stop the COM motion of the crystal, and it seems ok again, > > just like what I have found in the simulation system with that crystal > > only > > (with stopcm too). However, I get a lot of warnings in the log file as > > follows: > > Large VCM(group rest): 0.00015, 0.00094, -0.00022, > T-cm: > > inf > > Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm: > > inf > > Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm: > > inf > > Large VCM(group rest): 0.00007, 0.00034, -0.00231, > T-cm: > > inf > > Large VCM(group rest): 0.00007, -0.00043, -0.00213, T-cm: > > inf > > ...... > > I have not stop the COM motion of the group SOL, and I really do not know > > how to understand these warnings. I check the system again, everything > > seems > > alright except for these awkward warnings. I'm really out of ideas here. > > If > > anyone could give me some suggestions I would really appreciate it! Thanks > > for your time. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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