Thank You Jason
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
On Wed, Sep 23, 2015 at 1:28 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 - 11:00:02 PDT
