[gmx-users] infinite molecule problem - Follow up info

Bo Zhou zhoubo81 at gmail.com
Sun Apr 6 16:31:05 CEST 2008

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
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 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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