> >
> > 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.
>
For example, given the density of water is 0.99 g/cm^3, I want to know how
many
water molecules are in a box of size, say, 10 angstrom. So I will need
1 atomic mass unit = ?? gram conversion numbers.
Similary, with Coulomb law, the potential between two electrons is:
e^2
V(r) = k -------
r
My question is, what's the value of "k" in AMBER ?
> >
> > 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.
>
Let me clarify my question: vdW interactions are neglected (0) when the
distance is beyond
"cut", but simple neglection introduces discontinuities in the potential. So
the vdW potential is modified to make it smoothly go to 0 at "cut". My
question is, if AMBER has smooth vdW potential
function, how is it implemented ? Does it use switch function, or does it
use shift ?
Thanks for the answer. I realize my question is not clearly stated, sorry
for the confusion.
Clark
>..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
