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 >
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