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): 0.7, 0.00034, -0.00231, T-cm:
inf
Large VCM(group rest): 0.7, -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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