Dear Amber Users,
I'm trying to use a flag for restraining some atoms (NTR flag).
The Amber's manuals(version 6) says that the specified atoms are
restrained with a harmonic potential in this flag.
But, the manual also says that the unit of this harmonic force
constants is 'kcal/mol'.
I think this function is
E(x)= k*(x - x0)^2.
k is a harmonic force constant. x is a coordinate of atom
and x0 is an original coordinate of atom (from "refc" file).
If E(x) is potential energy, I think that the unit of force constant,k
should be energy / (length^2).
Could you kindly tell me the equation of restrain function
and the unit of force constant correctly?
Thank you for your help in advance.
Sincerely yours.
Chigusa Kobayashi
-----
Chigusa Kobayashi
Department of Physics,
University of California at San Diego
9500 Gilman Dr. La Jolla, CA, 92093-0319, USA
mail: chig_at_curio.ucsd.edu
Received on Thu Sep 06 2001 - 13:23:14 PDT
