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

[tuyusong]

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:

 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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