[gmx-users] angular COM removal

[XAvier Periole]

On May 9, 2009, at 12:47 PM, 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).
>> - 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?
Yes, indeed. But according to Berk's earlier comments on a related  
problem this
should be fine.
Note that the warning concerning the use of angular COM removal and DD  
did not
appear in grompp.
>
>
>> 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