From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Jul 18 2013 - 11:25:43 CDT
The question was about preventing a non-globular protein in a rectangular
box from rotating into a position where it can interact too strongly (or
even collide) with its images. Post-processing the trajectory won't help
against that.
On 07/17/2013 11:05 PM, Boyang Wang wrote:
> Hi Thomas,
> you can write a program to wash out the rotations, and process the
> trajectory by the program while the dynamics is saving the trajectory.
> Boyang
>
>
> On Thu, Jul 18, 2013 at 10:31 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> <mailto:giacomo.fiorin_at_gmail.com>> wrote:
>
> 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
>
>
>
>
> On Wed, Jul 17, 2013 at 10:18 PM, Thomas Albers
> <talbers_at_binghamton.edu <mailto: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
>
>
>
>
>
> --
> Boyang Wang, Ph.D.
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