VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jan 09 2012 - 05:11:19 CST

Hi Aaron,

That should be fine. The orientation bias is orthogonal to the
protein's internal coordinates.

Jerome

On 9 January 2012 01:30, Aaron Oakley <aarono_at_uow.edu.au> wrote:
> Greetings all,
>
> I'd like to perform an ILS calculation on a small protein
> that undergoes significant rotation during a 6 ns simulation.
> As I understand it, the tcl script produced by VMD corrects for
> molecule translation but not rotation.
>
> If I use the new collective variables facility in NAMD to prevent
> rotation of the molecule, will this bias the calculation in an unacceptable
> way?
>
> Thanks,
>
> a++
>