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

[David van der Spoel]

tuyusong wrote:
> 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.
yes. that should work.

> 
> 
> -----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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