AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 13 2005 - 10:23:17 CDT

On Tue, Apr 12, 2005, Nelson Fonseca wrote:

> "Xin Hu" <hux_at_mail.rockefeller.edu> escreveu:
> >>Did you compile nmode with double_precision?
> >>maybe its the solution for your problem.

I think people may be getting sidetracked here. The nmode program is always
compiled in double precision (as is all of Amber). You may be thinking about
compiling for 64-bit architectures, to allow very large memory use. But you
should only consider doing this after you are thoroughly familiar with the
operation of these programs on smaller problems. I would guess that most
attempts to do normal mode calculations on systems with more than 10,000
(even 5,000) atoms end up being more frustrating than scientifically
illuminating.

...dac

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