Re: Preventing rotation of a protein

From: Axel Kohlmeyer (
Date: Thu Jul 18 2013 - 11:32:28 CDT

On Thu, Jul 18, 2013 at 6:21 PM, Thomas Albers <> wrote:
> Hello!
>> Hello Thomas, the bias is only on the overall rotation, not on the internal
>> degrees of freedom: any force applied to the orientation colvar doesn't have
>> a projection along vectors that would change the internal structure of the
>> protein.
> Yes, but aren't the forces that are applied through the harmonic
> restrains acting only on the backbone?
> OK, one can argue that the random forces that cause the protein to
> diffuse away from its original orientation act only on the exterior,
> and the force applied to the backbone is of the same order of
> magnitude.
> I'm just slightly concerned that the colvar applies forces only to the
> backbone, and that might introduce systematic error.

please keep in mind, that any kind of rotation of that kind will be
*very* slow and thus you would need only a rather weak restraining
force. i would say that the error introduced by that, if any, would be
negligible compare to many of the other errors that your simulation
has. starting from finite size effects due to choosing a small box and
ewald/pme summation artifacts from not having a spherical box (or
rather as close as possible to spherical).


> Regards,
> Thomas

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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