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

[Bo Zhou]

When I stopCM of the whole system, all running is ok, but I found the
infinite surface oscillating along the xy plane collectively and frequently,
so there were too much inconsistent shifts. Then I stopCM of the surface
only, I get a lot of warnings about the Large VCM(group rest) (group rest =
SOL in my system). Thanks for your attention.

> 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.