[gmx-users] angular COM removal

[David van der Spoel]

David van der Spoel wrote:
> XAvier Periole wrote:
>>
>> Dears,
>>
>> I am asking for the angular removal of the COM motion of a protein 
>> assembly
>> in gromacs-4.0.4.
>>
>> - grompp gives a strange warning:
>>
>> checking input for internal consistency...
>>
>> WARNING 3 [file md.mdp, line unknown]:
>>   Removing the rotation around the center of mass in a periodic system
>>   (this is not a problem when you have only one molecule).
>>
In addition, this is not a strange warning, because this may introduce 
artifacts. In particular when you have water as well, you are basically 
violating Newton's second law (Fji = -Fij). One could argue that grompp 
should look into whether you have one molecule or not.

>> - the lines are:
>>
>> nstcomm                  = 1
>> comm-mode                = angular
>> comm-grps                = protein
>>
>>
>> Then the nstcomm and comm-mode appear to be correctly defined in the 
>> tpr file
>> generated. However during the run the angular removal of the COM is 
>> clearly not
>> done. The protein assembly is rotating ...
>>
>> Any reason for this?
>>
> Is this in parallel with DD?
> 
> 
>> XAvier.
>>
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> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se