AMBER Archive (2003)

Subject: AMBER: basic questions

From: Wei Wang (clark50236_at_hotmail.com)
Date: Mon Dec 01 2003 - 17:02:52 CST


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

_________________________________________________________________
Is there a gadget-lover on your gift list? MSN Shopping has lined up some
good bets! http://shopping.msn.com

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu