[gmx-users] Warning message with 3.3.3 but not with 3.3.1

[tuyusong]

> Bo wrote:
> Thanks David. So to speak, as the center of mass of group SOL is not
> free to move, we do not need stopcm to it. Another question is, does
> it would be problematic in long time simulation without stopcm in such
> situation, I mean the systematic errors caused by center of mass
> motion. Thanks for clarification.
> 
For a system with freeze group, we should not use any removal of com
motions, and this system should still work.
I don't find this relevant descriptions in gmx-manual, and it may be added
into it.
Yusong

> >
> > tuyusong wrote:
> > > Even in the system with position-restrain, when only removing com of
SOL
> > > group, gmx 3.3.3 also give the same error information as Bo:
> >
> > you can not only remove the com motion of one group. it is all (in one
> > or more groups) or nothing.
> > >
> > >  Large VCM(group rest):      0.00001,     -0.00002,     -0.00000,
> T-cm:
> > >  Inf
> > >
> > > Yusong
> > >
> > > -----Original Message-----
> > > From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]
> > > On Behalf Of David van der Spoel
> > > Sent: Thursday, April 17, 2008 3:21 AM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1
> > >
> > > Bo Zhou wrote:
> > >> Hi gmx-users,
> > >>
> > >> I want to simulate a solid/water interface. I just freeze the solid
> > > surface,
> > >> and let the water molecules free to move. Here is a part of my mdp as
> > >> follows:
> > >>
> > >> comm-mode     = linear
> > >> nstcomm       = 10
> > >> comm-grps      = SOL
> > >>
> > >> tcoupl          = Berendsen
> > >> tc-grps         = SOL Solid
> > >> tau-t           = 0.1 0.1
> > >> ref-t           = 298 0
> > >>
> > >> Same system and same sets were tested both in gmx 3.3.1 and gmx
3.3.3.
> > >> Following message in the log file was printed in the log file with
gmx
> > >> 3.3.3, but not with gmx 3.3.1.
> > >>
> > >> Large VCM(group rest):      0.00001,     -0.00002,     -0.00000,
> T-cm:
> > >> inf
> > >>
> > >> Large VCM(group rest):      0.00001,     -0.00003,     -0.00000,
> T-cm:
> > >> inf
> > >>
> > >> Large VCM(group rest):     -0.00000,     -0.00003,     -0.00000,
> T-cm:
> > >> inf
> > >>
> > >> I wonder whether it is reasonable to stopcm or not. Would it cause
any
> > >> non-physical artifacts? Thanks for suggestions.
> > >
> > > stopcm tries to change the velocity of the rest group (solid) as well.
> > > Unfortunately you can not turn this off for one group. I'm not sure
> > > while this is different from 3.3.1, but since you have a solid
reference
> > > you probably don't need to stopcm.
> > >
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> > >
> >
> >
> > --
> > David.
> >
> ________________________________________________________________
> ________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> >
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