Re: [AMBER] Help with ncsu_abmd flooding mode

From: Jason Swails <>
Date: Mon, 27 Aug 2012 14:16:26 -0400

On Mon, Aug 27, 2012 at 1:48 PM, Fabrício Bracht <> wrote:

> By fall out of use, you mean that the users are not asking questions
> about it? Or do you mean to say that it is not a tool that amber
> consider to be important anymore, and so it is doomed to disappear
> from future amber releases? Or even that there are better ways in
> amber to obtain free energies with regard to pulling processes?

Not many people ask questions about it, and the original developers no
longer actively develop it, to my knowledge. Nor do they answer questions
on this list about it. I'm not sure what will happen to it in the future
(will an active developer pick it up and carry it on? will it rot and
eventually be discarded if it starts to break other parts of actively
developed code?). However, as Brian mentioned, the best bet for using
these modules for the time being is to study the manual, try different
things, and look at the source code if all else fails.

I would also suggest looking through some of the NCSU tests in the
$AMBERHOME/test directory -- they will typically have sample input files
you can modify to your uses.

You can use Steered MD (using the 'jar' option) for free energies of
pulling processes, as well.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Aug 27 2012 - 11:30:03 PDT
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