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

[tuyusong]

David wrote:
> you can not only remove the com motion of one group. it is all (in one 
> or more groups) or nothing.

Thank you for replying.
Do you mean, that it must be nothing when system has any freeze groups?
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 4:01 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

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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