On Mon, Dec 01, 2003, Wei Wang wrote:
>
> 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
I probably don't understand your question: if you want to convert kcal/mol
to kJ/mol, you multiply by 4.183, etc.
>
> 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 ?
>
Neither one: Amber ignores all vdW interactions where the distance is greater
than "cut", as specified in the input file.
...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Jan 14 2004 - 15:53:03 PST
