From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Wed Jul 17 2013 - 22:05:03 CDT
you can write a program to wash out the rotations, and process the
trajectory by the program while the dynamics is saving the trajectory.
On Thu, Jul 18, 2013 at 10:31 AM, Giacomo Fiorin
> 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.
> On Wed, Jul 17, 2013 at 10:18 PM, Thomas Albers <talbers_at_binghamton.edu>wrote:
>> 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?
-- Boyang Wang, Ph.D.
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