From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Dec 10 2012 - 16:29:18 CST
The force constant will of course depend on the strength of the underlying
potential landscape. Perhaps you have a deep energy well located in the
direction of 7.3 that is overpowering the restraints.
Certainly for something like a ligand diffusing around in solution far from
the binding site, 1 kcal/mol*A^2 is enough to keep it fairly firmly within
the bounds, but maybe your situation is much different?
On Mon, Dec 10, 2012 at 5:15 PM, DAI, JIAN <jdai2_at_fsu.edu> wrote:
> Dear NAMD fellows:
> We are calculating the free energy landscape of a protein using two
> distance restraints that describe the distance between two domains of the
> The problem is: I noticed that the boundary values of the colvars have
> constantly exceeded the restraint values. Although the force constants that
> are put on these distances are small, i.e., 1 kcal/mol A^2, the distances
> should not exceed the upperboundary and lowerboundary too much, shouldn't
> they? In the simulation, for example, when the boundary is set at
> lowerboundary 9.0 and upperboundary 10.0,
> the actual value of the second colvar drops down to even 7.3, which I
> think is way too low.
> The configuration and colvars definition files are attached. Should we
> expect to see that these distance values exceed the boundary values or a
> stronger force constants will solve this problem? However, I've seen in
> another work that also uses a force constant of 1 (Wereszczynski and
> McCammon, 2012, PNAS).
> Thanks in advance.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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