[gmx-users] angular COM removal

[XAvier Periole]

On May 9, 2009, at 12:50 PM, David van der Spoel wrote:

> 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.
Agreed. But the phenomenon I observe is not affected (it happens with  
both setups
with identical characteristics) and the trick saves a lot of computer  
time (amount of solvent)!
>
>>> - 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.
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before  
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use thewww  
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> -- 
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php