[AMBER] Two fragments minimization

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Sun, 13 Feb 2011 13:23:00 -0800 (PST)

I am trying to study the electrostatic and VDW interactions between two fragments. At the same time, I would like to freeze each fragment, i.e. minimize only the distance between the two fragments based on the non-bonded interactions. I applied a harmonic force on each fragment of 0.2 kcal/mol and minimized the system. Is that a right way?, also I was wondering how should I account the effect of the applied harmonic force. How can I ensure the harmonic force has no effect on the net non-bonded interactions between the two fragments.
Any kind of help would be highly appreciated.
Thanks in advance


AMBER mailing list
Received on Sun Feb 13 2011 - 13:30:04 PST
Custom Search