Dear AMBER users,
I am trying to learn how to set up QM/MM simulations for reaction catalyzed by enzyme. I would performe umbrella sampling on my reaction coordiate (RC). Since my system involved in multiple bonds forming/bonds breaking, I wonder how to put a restraint on the differences of several key distanaces in my RC? AMBER can do simple distance constraint and angles, torsion angles as well. But what I need, for example, I have 4 key distances r1 r2 r3 r4, how to implement an harmonic restraint with a formular like k[(r2-r1)^2+(r4-r3)^2] to performe unbrella sampling in AMBER?
Any help will be highly appreciated. Thanks!
Iccy
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Received on Fri Apr 29 2011 - 11:30:03 PDT
