[gmx-users] infinite molecule problem - Follow up info
Computational Structural BIology
xwxnju at gmail.com
Mon Apr 7 16:50:49 CEST 2008
Stop COM of the whole system?
2008/4/6 Bo Zhou <zhoubo81 at gmail.com>:
> 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
> 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
> 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
> 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
> (with stopcm too). However, I get a lot of warnings in the log file as
> Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm:
> Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm:
> Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm:
> Large VCM(group rest): 0.00007, 0.00034, -0.00231, T-cm:
> Large VCM(group rest): 0.00007, -0.00043, -0.00213, T-cm:
> 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
> alright except for these awkward warnings. I'm really out of ideas here.
> anyone could give me some suggestions I would really appreciate it! Thanks
> for your time.
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