AMBER Archive (2006)

Subject: AMBER: hessian calculation

From: sebnem (
Date: Tue Mar 28 2006 - 15:48:19 CST

I have a question about using icons option in nmode in amber7.
 I carried out a minimization in nmode with some restraints on
particular part of the molecule .Then for the part of hessian
calculation, I used two different inputs.
One of them has the same force constant for restraints as the
minimization part , and in the other one I used a larger force constant
for restraint.
The problem is that I see a difference in the the part of the hessian
which actaully doesn't correspond to the restrained part of the
molecule. My question is how the force constant on the restrained atoms
can effect the second derivative of the potential with respect to the
non-restrained coordinates?
I will really appreciate your comments,

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