[gmx-users] 6 degrees of freedom

[Anton Feenstra]

jozef hritz wrote:
> 
>         Hi Everybody,
> I need to run long simulation of protein and I inertial motion is not
> important. How is it possible to let only 6 degrees of freedom for protein
> (3 for translation and 3 for rotation)?

By default, nstcom in your .mdp file is set to 1, this will remove
COM (center of mass) motion every step. By setting it to -1, the
coordinates of your system are fitted onto the previous coordinates
every step, which effectively removes overall rotation. It is possible
that the fitting procedure when performed every step, introduces
artefacts.

-- 
Groetjes,

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