Re: [AMBER] Help with ncsu_abmd flooding mode

From: M. L. Dodson <>
Date: Mon, 27 Aug 2012 16:05:12 -0500

On Aug 27, 2012, at 1:16 PM, Jason Swails wrote:

> 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.
> HTH,
> Jason

Hopefully, if it is to go bye-bye whoever holds copyright will see fit to
release it under a "free" license such as BSD or even GPL. I might even
work up enough energy to see if I could modify the code to make it linkable
to nab, if it were to become unencumbered. Since I don't (or plan to: I'm
retired) hold a license for current or recent versions of AMBER, I'm

I find the syntax of the ncsu way of doing things enormously easier to use
than the "NMR restraint" extensions that do a subset of the ncsu stuff. I
would really like to see this code continue in some guise.

Bud Dodson
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Mon Aug 27 2012 - 14:30:03 PDT
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