[gmx-users] comm-mode = Angular don't work

[Anton Feenstra]

Alan Wilter Sousa da Silva wrote:
> 
> Hi List,
> 
>         I'm using GMX 3.1.3.
> 
>         I set in my mdp file the option:
> comm-mode = Angular
> 
> (new and different from nstcomm option of GMX 3.0.x, right?)
> 
> when running grompp I get:
> [...]
> WARNING 1 [file myfile.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).
> calling /lib/cpp...
> [...]
> 
> and mdrun gives errors,
> 
> When I change from Angular to Linear it works ok.
> 
> My system is in a box of water so I believe that comom-mode = Linear is
> equivalent to the old option nstcomm = 1 (positive number, while negative
> is only for vacuum simulations, not my case).
> 
> Are these observations corrects?

Sounds right. Like grompp says, removing rotation in a periodic
system is probably not right, except when you have e.g. no solvent.
Since you have solvent, you need to keep the periodic boundaries
connected over the box sides. So things will break when mdrun tries
to remove the overall rotation, since that kills the periodic
continuity.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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