[gmx-developers] Large VCM(group rest): Temp-cm: inf

[David van der Spoel]

Carsten Kutzner wrote:
> Am 18.09.2008 um 17:43 schrieb Berk Hess:
> 
>> Hi,
>>
>> I have added a check on group_ndf.
>>
>> But how can you have a vcm group with non-zero mass, but with zero 
>> degrees of freedom?
>>
> Hi,
> 
> In the mdp file just a single comm-grp was defined, but in the debugger 
> I saw that
> the number of groups is 2, with the second group having no name. Maybe 
> thte number
> of groups should be 1 in that case anyway?

grompp automatically makes a rest group, could be an error there.
Note that stopcomm-ing part of the system affects energy conservation 
and also dynamics, because forces are not conservative anymore.

> 
> Carsten
> 
>> Berk
>>
>> Carsten Kutzner wrote:
>>> Hi,
>>>
>>> we appear to have another small problem with the CVS version.
>>> For a protein in water system, where comm-grps=Protein is
>>> chosen we continuously get the following line outputted to log:
>>>
>>> Large VCM(group rest):      0.00005,     -0.00002,     -0.00004, 
>>> Temp-cm:          inf
>>> Large VCM(group rest):      0.00006,     -0.00003,     -0.00004, 
>>> Temp-cm:          inf
>>> Large VCM(group rest):      0.00006,     -0.00003,     -0.00003, 
>>> Temp-cm:          inf
>>> Large VCM(group rest):      0.00006,     -0.00004,     -0.00002, 
>>> Temp-cm:          inf
>>> Large VCM(group rest):      0.00006,     -0.00005,     -0.00001, 
>>> Temp-cm:          inf
>>> ...
>>>
>>> This happens also for the non-MPI mdrun. The problem is that in 
>>> check_cm_grp (vcm.c)
>>> the number of degrees of freedom for the 2nd group are zero. Thus
>>>
>>> Temp_cm = 2*ekcm/vcm->group_ndf[g];
>>>
>>> becomes infinity, triggering the message. This is just an output 
>>> problem, since
>>> nothing needs to be done to the COM of the second group anyway. 
>>> However, the md.log files
>>> become HUGE when this is outputted at every step.
>>>
>>> Carsten
>>>
>>>
>>>
>>>
>>
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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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