Hi, Chunli
String method can only give the least free energy path in the phase space,
cannot
give the whole landscape of free energy.
To get the PMF, you can use umbrella sampling, or the ABMD method by &abmd
module,
you can check the manual for details.
Best
Feng
On Thu, Aug 17, 2017 at 1:42 AM, Chunli Yan <utchunliyan.gmail.com> wrote:
> Hello,
>
> After I finished the simulation by using string methods, I got a lists of
> output file for each image (mdcrd*, rst*, stsm* and so on). In amber
> manual:
>
> When you get the biasing potential (*.nc file), you can always use the
> nfe-umbrella-slice utility to access
>
> its content and get a friendly-written ASCII file from which one can obtain
> the free energy map. The output
>
> is the free energy value, which is the opposite of the biasing potential (
> f = U (units kcal*=*mol )). The
>
> nfe-umbrella-slice utility has been included in AmberTools.
>
>
> Usage: nfe-umbrella-slice [options] bias_potential.nc
>
>
> I am wondering how to compute free energy along the image. How to get the
> biasing potential.
>
>
> Thanks,
>
>
> Best,
>
>
> *Chunli*
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Thu Aug 17 2017 - 16:00:03 PDT
