Re: [AMBER] Regarding AMBER help command and Ewald Namelist Variables Specificat​ions

From: case <>
Date: Tue, 15 Feb 2011 08:24:28 -0500

On Mon, Feb 14, 2011, Naveen Samala wrote:
> 1. I would like to know the command that can be used to bring the help
> manuals or topics about a particular namelist/variable like &ewald , nfft1
> etc.

You can consult the index for individual variables, but carefully reading
section 2.7.2 is likely you best option.

> 2. I would be grateful to you if you can provide me more details(apart from
> user manual) about the &ewald specifications that can used in calculating
> the energies with least error or in other way the various possibilities of
> specifying the variables in the &ewald namelist.

You should study refs. 31-36 for more details. Please note that the defaults
have been carefully chosen: you might just experiment with relatively small
deviations from those.

You might also want to look at the following paper, which talks a fair amount
about errors and accuracy:

%T Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald
Method Adding Great Versatility
%A D.S. Cerutti
%A R.E. Duke
%A T.A. Darden
%A T.P. Lybrand
%P 2322-2338
%J J. Chem. Theory Computat.
%V 5
%D 2009


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Received on Tue Feb 15 2011 - 05:30:07 PST
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