There are lots of ways. There's an entire section of the amber11 manual
that's devoted to "sampling and free energy". Likewise for earlier versions
of the manual. In Amber11.pdf, this is chapter 4. Examples include steered
MD, umbrella sampling, adaptively biased MD, REMD, etc. The Amber manual
also supplies references about the theory of the method and how it's
implemented, so perusing those will help as well.
Good luck!
Jason
On Thu, Oct 28, 2010 at 3:11 AM, fancy2012 <fancy2012.yeah.net> wrote:
> Dear amber users,
> How could I get the free energy landscape from an amber coordinate? Because
> I want to get the model, which is at the bottom of the energy surface.
> Thanks very much!
>
> All the best,
> fancy
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Oct 28 2010 - 06:30:03 PDT
