From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Thu Dec 11 2003 - 18:21:48 CST
Hi Zhilei,
On Thu, 11 Dec 2003, zhilei chen wrote:
> Dear namd user,
>
> This is a question about the harmonic constraints force constant. Can
> anyone tell me what is the unit of this force constant and what is the
> equation used to calculate this force?
I believe the units of the force constant are kcal/(mol*Angs^2) and the
equation used is a harmonic one, F = (1/2)k*x^n, where x is distance from
equil position and n is set by the NAMD command consexp (default 2, as you
might expect).
> If I want to set up energy
> minimization with harmonic constraints on the CA, are there any rules
> about what kind force constant I shall use?
"Rules? Where we're going, there are no rules." Sorry. A reasonable
value is around 5 for the force constant, but in general it highly depends
on what you want your atom to be able to do. I don't know exactly what
you will do, but keep in mind that you can set up a run with high force
constant, let the atoms around equilibrate, and continue that run with
another config file with a small force constant. In this way, you can
gradually release the constraints.
>
> Thanks a lot
>
> zhilei
>
No Problem,
Tim
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