On Jun 15, 2013, at 9:29 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi,
>
> I wish to ask if there is a way to generate free energy landscapes with ptraj? Not the PMF diagram, but those that are coloured according to energy depths, so as to allow easy identification of deep energy wells.
As far as I know only cpptraj can do that. However, the PMF diagram and the colored maps are the same thing, the only difference being that the colored diagrams are typically 2-D surfaces (i.e. there are two reaction coordinates) whereas the PMF diagram is only a 1-D curve (i.e. there is only one reaction coordinate.
Cpptraj can histogram data, and has an option to convert that histogram into a free energy (by taking the logarithm of the ratio of each bin's occupancy with the most occupied bin and multiplying it by kT). You can use some plotting program, like gnuplot, to color the resulting surface for a 2-D histogram. look at the histogram commands in the cpptraj part of the AmberTools 13 manual. (And make sure you have an up-to-date AmberTools 13 installation, which is free to download).
This is only one way to make a PMF (and typically a bad way if there are a lot of high barriers in the surface, since the sampling is unbiased). If you do biased sampling like umbrella sampling, you will need to generate the unbiased PMF another way.
HTH,
Jason
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jun 15 2013 - 12:00:02 PDT
