AMBER Archive (1999)

Subject: ANAL Questions!

From: Dat H. Nguyen (nguyend_at_chem.ucdavis.edu)
Date: Wed Jul 14 1999 - 16:09:01 CDT

Dear AMBER Users:

I am using ANAL to calculate the energy decomposition of chemically
identical system but different configurations. I was just wondering if
anyone can provide me with answers for the following questions:

1. ANAL does not have PME feature incorporated into it, so how is
long-range electrostatic interactions handled? Will it be ignored if the
distance between 2 charges greater than the cutoff distanceb (using the
pairlist)? If so, How big is the cutoff distance sufficient in order to
achieve acceptable accuracy (e.g. Rcut = 15.0 (A)?)

2. ANAL contains bug, as shown on AMBER webpage, that is not consistant
with SANDER in computing energy. Can anyone tell how serious it is? I'd
like to use ANAL to compare energies of different sub-systems. Can
anyone give me your opinions on this?

Thank you very much.

Sincerely,

Dat
***********************************************************************
* Dat H. Nguyen *
* -------- *
* Chemistry Department | Biology and Biotechnology Research Prog.*
* University of California | Lawrence Livermore National Laboratories*
* One Shields Avenue | Mailstop L-452 *
* Davis, CA 95616 | Livermore, CA 94550 *
* Phone: (530)-752-3242 | *
* *
* E-mail: nguyend_at_chem.ucdavis.edu *
* URL: http://www-chem.ucdavis.edu/~nguyend *
***********************************************************************