[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
> 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.
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