AMBER Archive (2008)

Subject: AMBER: Force field in water and in vacuum ??

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu May 22 2008 - 10:46:15 CDT

Hi
For one molecule, will Amber give the same set of force field parameters to this molecule no matter this molecule is put in
water or in vacuum?
The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum.
So, will the force field parameters be changed/ adjusted in water than in vacuum?

How does Amber set the force field parameters for the molecule?
I mean..... are the force field paramters determined in local or in global?
Could I change parts of the force field parameters which I found from the published paper?
Or, I could not change parts of the force field parameters; instead, I have to change the whole set of the force field
parameters???

Thank you
Lin

 

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