Re: rotational restrains

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Jun 04 2010 - 16:03:13 CDT

Hi Arturas,

The colvars module will let you do that, if you use the "orientation"
colvar component, and a harmonic bias. See the user's guide as well as
this example:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11245.html

Note that in the example above, the problem was that the coordinate
was defined on thousands of atoms. If you select a few tens of atoms,
distributed across your molecule, it should work well and efficiently.
Choosing the force constant is up to you - the unit is
kcal/mol/[quaternion unit]^2, where the quaternion "unit" is really a
unitless number, so a change much smaller than unity in quaternion
coefficients will represent a small rotation. In any case, the best
way is to test it for yourself.

Cheers,
Jerome

On 4 June 2010 20:34, Ziemys, Arturas <Arturas.Ziemys_at_uth.tmc.edu> wrote:
> Hi,
>
> Could anyone advise a way to restrain rotations of molecule, but letting it be free in translation  ?
>
> Arturas
>
>

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