Re: AMBER: Sander TI with NTR = 1.

From: David A. Case <>
Date: Thu, 16 Sep 2004 07:56:48 -0700

On Wed, Sep 15, 2004, Chunhu Tan wrote:
> I want to calculate the electrostatic solvation free energy of a
> residual (which is position "constrained") in water. I know ibelly cannot
> work with ICFE, so I use NTR=1. My question is, if I can use a large
> force constant (say, 500) because I want to "frozen" the residual? If this
> strong restraint will affect the result of DV/DL? If yes, how can I
> estimate it?

A force constant in the range of 10-50 will keep the residue very close to
its initial position, and should not cause instabilities in the MD
integration. You could always "do the experiment": try calculations with
varying values for the force constant, and see what happens.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Sep 16 2004 - 16:53:00 PDT
Custom Search