I have the following basic questions to ask regarding AMBER implementation:
1. What's the unit values used in AMBER ?
1 AMU = ? kilogram,
1e = ? Coulomb (or if V= f * q1*q2 / r^2, what is the value of f ?)
1 kcal/mol = ? Joule
2. the van der Waals potential generally has a cutoff radius,
There are two implementations: one is using swith function (v -->
v*swtich); another is using
shift function (v --> v - shift).
my question is which implementaion does AMBER use ?
I have looked through the manual and FAQs, but don't find the answer yet.
Sorry, if the answer has been posted.
Clark
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Received on Wed Jan 14 2004 - 15:53:03 PST
