[gmx-users] Re: 6 degrees of freedom

[Anton Feenstra]

jozef hritz wrote:
> 
>         Dear Anton,
> 
> > 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.
> 
> There is some misunderstanding. What I wish is to keep (not remove) these
> 6 degrees of freedom (3 translation, 3 rotation) and remove all other
> degrees of freedom to be able to simulate much longer time. But I don't
> know how to do it. Any idea?

Yes. Don't simulate. You can easily calculate all equilibrium properties
for these degrees of freedom.

-- 
Groetjes,

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