Re: AMBER: question about delphi and UHBD

From: Ray Luo <>
Date: Tue, 28 Sep 2004 10:58:11 -0700 wrote:

>Dear amber users,
>I try to use delphi and UHBD to do MM-PBSA. For the same system, I get
>the same coulombic energy, but reaction field energies are totally
>different. Input parameters(grid size/dimension, focusing,
>internal/solvent dielectric, temperature) are same except convergence
>threshold. In UHBD, this value is 1 X 10E-6 (it is default value. I
>don't know how to change it), and convergence is achieved at 200 steps
>or so:
Aside from different numerical implementations of molecular surface and
finite difference solvers, Delphi and UHBD also use very different
methods to compute reaction field energies. So in the end, you can't get
agreement at all for a complex molecule, such as a large protein.


Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Sep 28 2004 - 19:53:01 PDT
Custom Search