From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jul 27 2011 - 01:40:24 CDT
Curvature is defined locally, but simple derivations for the bending modulus
presume a constant curvature throughout the chain. I'm not terribly worried
about twisting motions, which ideally would be averaged over anyway. The
problem with defining just one angle is that the final structure won't be a
semi-circle but rather a triangle of sorts.
From: heninj_at_gmail.com [mailto:heninj_at_gmail.com] On Behalf Of Jérôme Hénin
Sent: Wednesday, July 27, 2011 1:30 AM
To: JC Gumbart
Cc: namd-l list
Subject: Re: namd-l: using colvars for bending modulus?
I'm not very familiar with this, but isn't curvature a local property?
Here you want a kind of mesoscopic measurement on the whole chain, so
if the chain twists, it gets complicated. My best guess for a simple
yet relevant quantity is the angle between three groups, two ends and
the center of the chain.
On 26 July 2011 22:43, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Has anyone considered how to use a collective variable to measure a PMF as
a function of radius of curvature for a polymer? I thought about something
like a combination of angle terms between successive links, but it wouldn't
necessarily stay planar.
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