Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file?

[Radovan D. <dv...@mp...>]

On 04.06.2014 16:54, Ooker wrote:
> > From definition: Poisson-Boltzmann equation becomes at zero 
> concentration of ions around the molecules Poisson equation (right?).
>
> This is new. After googling around, I can't find any support for this. 
> I think the Wikipedia's definition is good enough: The 
> Poisson–Boltzmann equation is a differential equation that describes 
> electrostatic interactions between molecules in ionic solutions.
>
@ According to the formula at 
http://en.wikipedia.org/wiki/Poisson%E2%80%93Boltzmann_equation, putting 
ci - i.e. concentration of the ion i at a distance of from the solute 
(what I know as bulky concentration) - converts the equation directly to 
Poisson equation (http://en.wikipedia.org/wiki/Poisson's_equation) (or 
wrong?)

@ In my opinion - that describeselectrostatic 
<http://en.wikipedia.org/wiki/Electrostatic>interactions between 
molecules inionic solutions 
<http://en.wikipedia.org/wiki/Ionic_solution> - is not correct. It 
describes electrostatic potential according to the distribution of 
charges and properties of media/space. In order to describe the 
interaction free energy has to be calculated out of that potential what 
is implemented and used in APBS and/or DelPhi (or not?)

> >The only issue is the permittivity of molecule/protein and 
> solution/vacuum. When I played with that, it has only scaling effect 
> on the potential (right?).
>
> What is scaling effect? Did you mean when moving from large scale to 
> small scale, somethings didn't work?
@ Changing the permittivity of solute or solution just scaled uniformly 
the values of electrostatic potential at each grid point. But this 
conclusion is without guarantee as it was a long time ago....

>
> >To be correct, direct summing through the charges did not give exact 
> values of potential obtained from APBS (I assume that because of 
> finite elements) but interestingly, APBS was faster for large 
> molecules - even when the summing was implemented in C (explanation?).
>
> Nathan knows this best.
>
> >
> > Regards,
> > Radovan
> >
> > On 04.06.2014 07:14, Ooker wrote:
> >
> > So you mean that the Boltzmann distribution is necessary if there 
> are ions around the molecule. Otherwise it is not, am I right?
> > On 6/4/2014 10:22 AM, Travis Mackoy wrote:
> >
> > ‎Hello,
> >
> > Consider the ion distribution around the molecule. The PQR contains 
> information regarding the molecule.
> >
> > Best Regards,
> >
> > Travis Mackoy
> >
> >
> >   Original Message
> >
> > From: Ooker
> > Sent: Tuesday, June 3, 2014 11:13 PM
> > To: Baker, Nathan; apb...@li... 
> <mailto:apb...@li...>
> > Subject: Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann 
> equation if I only need to build electrostatic potential from a PQR file?
> >
> > I know that the analytic solution is only available for simple 
> cases, however it is still possible to have the solution in numeric, 
> right? We don't need to have a analytic solution.
> >
> > Ooker.
> > On 6/4/2014 10:07 AM, Baker, Nathan wrote:
> >
> > Hello –
> >
> >
> >
> > The analytic solution to the Poisson equation is only available for 
> highly simplified geometries or uniform dielectric coefficients.
> >
> >
> >
> > Thanks,
> >
> >
> >
> > --
> >
> > Nathan Baker
> >
> > Laboratory Fellow and Technical Group Manager
> >
> > Applied Statistics and Computational Modeling
> >
> > Pacific Northwest National Laboratory
> >
> > +1-509-375-3997
> >
> > http://www.linkedin.com/in/nathanandrewbaker/
> >
> >
> >
> > From: Ooker [mailto:gan...@gm... 
> <mailto:gan...@gm...>]
> > Sent: Tuesday, June 03, 2014 2:47 AM
> > To: apb...@li... 
> <mailto:apb...@li...>
> > Subject: [apbs-users] Is it neccesary to use Poisson - Boltzmann 
> equation if I only need to build electrostatic potential from a PQR file?
> >
> >
> >
> > Hello,
> >
> > I would like to ask you a question. If the PQR file contain the 
> position and charge of every atom in it, is it really necessary to use 
> PBE? The Boltzmann distribution is useful if you don't know how to 
> build the charge density. If you have position and charge of every 
> point, you can construct it, therefore easily to find the potential 
> just by using Poisson equation.
> >
> > Thank you.
> >
> > ‎
> >
> > From: Ooker
> > Sent: Tuesday, June 3, 2014 11:13 PM
> > To: Baker, Nathan; apb...@li... 
> <mailto:apb...@li...>
> > Subject: Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann 
> equation if I only need to build electrostatic potential from a PQR file?
> >
> > I know that the analytic solution is only available for simple 
> cases, however it is still possible to have the solution in numeric, 
> right? We don't need to have a analytic solution.
> >
> > Ooker.
> > On 6/4/2014 10:07 AM, Baker, Nathan wrote:
> >
> > Hello –
> >
> >
> >
> > The analytic solution to the Poisson equation is only available for 
> highly simplified geometries or uniform dielectric coefficients.
> >
> >
> >
> > Thanks,
> >
> >
> >
> > --
> >
> > Nathan Baker
> >
> > Laboratory Fellow and Technical Group Manager
> >
> > Applied Statistics and Computational Modeling
> >
> > Pacific Northwest National Laboratory
> >
> > +1-509-375-3997
> >
> > http://www.linkedin.com/in/nathanandrewbaker/
> >
> >
> >
> > From: Ooker [mailto:gan...@gm... 
> <mailto:gan...@gm...>]
> > Sent: Tuesday, June 03, 2014 2:47 AM
> > To: apb...@li... 
> <mailto:apb...@li...>
> > Subject: [apbs-users] Is it neccesary to use Poisson - Boltzmann 
> equation if I only need to build electrostatic potential from a PQR file?
> >
> >
> >
> > Hello,
> >
> > I would like to ask you a question. If the PQR file contain the 
> position and charge of every atom in it, is it really necessary to use 
> PBE? The Boltzmann distribution is useful if you don't know how to 
> build the charge density. If you have position and charge of every 
> point, you can construct it, therefore easily to find the potential 
> just by using Poisson equation.
> >
> > Thank you.
> >
> >
> >
> >
> >
> >
> > 
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