AMBER Archive (2003)

Subject: Re: AMBER: basic questions

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 02 2003 - 00:37:59 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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