From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jul 18 2013 - 06:00:19 CDT
.. which means that you can, and should, define the orientation using a subset of atoms. For proteins, alpha carbon atoms are often sufficient.
Jerome
----- Original Message -----
>
> 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.
>
>
> Giacomo
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> On Wed, Jul 17, 2013 at 10:18 PM, Thomas Albers <
> talbers_at_binghamton.edu > wrote:
>
>
> Hello!
>
> I have got a system with a 400 amino acid dimer that fits into a
> 128*96*96 A oblong water box. That's about 100K atoms. A cubic
> 128*128*128 water box would be about 200K atoms.
>
> If I restrain the rotation of the protein with an orientation colvar,
> as hinted at on p. 123 of the NAMD 2.9 manual there's a *substantial*
> speed penalty; IIRC it's so bad that I might as well drop the colvar
> and use a cubic box instead. However, in the recent protein-ligand
> binding tutorial (this one:
> http://www.ks.uiuc.edu/Publications/Stories/plbtutorial/ ) the colvar
> is defined only for the backbone of the protein, this is much faster,
> but I fear I might introduce bias in the internal degrees of freedom.
>
> Does anyone on the list have some input?
>
> Regards,
> Thomas
>
>
>
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