On Wed, Sep 23, 2015 at 12:05 PM, Rahul Ramesh <raramesh.umich.edu> wrote:
> Hey Jason
> I am trying to make sense of the equation given in " Constant pH MD in
> Generalized Born Implicit Solvent" by David Case.
> [image: Inline image 1]
> I understand that del G elec,ref is calculated from the Thermodynamic
> Integration. I am not able to get protonation state change for my system
> and I want to know how to find the del G elec which the simulation code
> calculates so that I can compare that value with my del G elec,ref and
> troubleshoot.
>
Take a single structure. It is the energy difference between that
structure in which the charges are set to 1 protonation state minus the
energy calculated when the charges are set to the other protonation state.
All you are changing are the partial charges. You can calculate this "by
hand" using ParmEd with the "energy" and "changeProtState" commands.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 23 2015 - 10:30:03 PDT
