<div>Stop COM of the whole system?</div>
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<div class="gmail_quote">2008/4/6 Bo Zhou <<a href="mailto:zhoubo81@gmail.com">zhoubo81@gmail.com</a>>:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear gmx users,<br><br>My previous question are:<br><br>>I want to simulate the solid/liquid interface, so I build an infinite<br>
inorganic molecule with pbc=full first. After I ran the system<br>> with vaccum (at the top of system) for a few ps, I found the crystal<br>oscillating along the xy plane collectively and frequently,<br>> so there were too much inconsistent shifts. I wonder if it is reasonable,<br>
if not, is there any solution for it? Any suggestions<br>> would be helpful. Thanks.<br><br>I have tested one system with infinite crystal only, and it turns out be to<br>quite stable (no collective motion has been found), but when I put some<br>
water molecules on it, the crystal surface turns out to be what I have said<br>above. Then I stop the COM motion of the crystal, and it seems ok again,<br>just like what I have found in the simulation system with that crystal only<br>
(with stopcm too). However, I get a lot of warnings in the log file as<br>follows:<br>Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm:<br>inf<br>Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm:<br>
inf<br>Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm:<br>inf<br>Large VCM(group rest): 0.00007, 0.00034, -0.00231, T-cm:<br>inf<br>Large VCM(group rest): 0.00007, -0.00043, -0.00213, T-cm:<br>
inf<br>......<br>I have not stop the COM motion of the group SOL, and I really do not know<br>how to understand these warnings. I check the system again, everything seems<br>alright except for these awkward warnings. I'm really out of ideas here. If<br>
anyone could give me some suggestions I would really appreciate it! Thanks<br>for your time.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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