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

[周波]

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.


>
> 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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