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

[David van der Spoel]

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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