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. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
