Re: Preventing rotation of a protein

From: Kenno Vanommeslaeghe (
Date: Thu Jul 18 2013 - 11:54:15 CDT

The forces needed to effectively counter the Brownian motion of a protein
are very subtle, and one could argue that their effect is likely smaller
than a lot of the other assumptions commonly made when running MD.
Applying these weak forces on a subset of atoms has been pretty routine
practice for a long time, so one would think if it has significant
effects, someone would have noticed already. I don't have any hard
evidence handy (maybe someone else here does), but I generally feel there
are worse things to worry about in a typical MD simulation.

On 07/18/2013 12:21 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.
> Regards,
> Thomas

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