If you are talking about without biasing, then it's pretty simple, but
probably not accurate.
You would just use something like ptraj in order to generate a big list of
the distance between that ion pair for each timestep in your simulation.
Then you would choose some kind of discreet distance for binning, say 0.1A,
and bin all your results in order to make a histogram. Normalize the
histogram to have a sum of 1.0, since it represents probability, and then
convert from probability to work or free energy, using dG = -RTln(Keq),
where Keq is your probability at each bin (I may have messed up that
equation, but you can probably google the correct one if I did). This
should give you a PMF.
This will likely be inaccurate because of sampling problems, and it would
be best to use a biased simulation technique unless you are quite sure that
your unbiased simulation captures all the of the relevant ensemble of
states.
~Aron
On Sun, Jul 22, 2012 at 3:03 PM, Rajendra Sharma <rajenbiotech.gmail.com>wrote:
> Dear All,
>
> I need to calculate PMF of a salt bridge to study if it is involved in
> helix stabilization or if helix stabilization is due to desolvation on
> mutation. Could any body suggest how to calculate PMF of a salt bridge in
> detail from the distance calculated over trajectories between the ion pair.
>
> Sincerely,
>
> Rajendras
> --
> Rajendra Sharma
> Junior Research Fellow,
> Computational Biophysics,
> *National Center for Biological Sciences,*
> (Tata institute of Fundamental Research)
> India.
> Mobile No. +91-9950675288
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Jul 22 2012 - 13:30:03 PDT
