apbs-users

 [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Ooker - 2014-06-03 09:47:17 Attachments: Message as HTML ```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. ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Baker, Nathan - 2014-06-04 03:07:32 Attachments: Message as HTML ```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:ganuongphap@...] Sent: Tuesday, June 03, 2014 2:47 AM To: apbs-users@... 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. ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Ooker - 2014-06-04 03:13:19 Attachments: Message as HTML ```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:ganuongphap@...] > *Sent:* Tuesday, June 03, 2014 2:47 AM > *To:* apbs-users@... > *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. > ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Travis Mackoy - 2014-06-04 03:38:25 Attachments: Message as HTML     ATT001.txt ```_______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Ooker - 2014-06-04 05:14:18 Attachments: Message as HTML ```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; apbs-users@... > *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:ganuongphap@...] >> *Sent:* Tuesday, June 03, 2014 2:47 AM >> *To:* apbs-users@... >> *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; apbs-users@... > *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:ganuongphap@...] >> *Sent:* Tuesday, June 03, 2014 2:47 AM >> *To:* apbs-users@... >> *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. >> > > ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Radovan Dvorsky - 2014-06-04 10:20:53 Attachments: Message as HTML ```H! From definition: Poisson-Boltzmann equation becomes at zero concentration of ions around the molecules Poisson equation (right?). Another point: as far as I remember, Coulomb electrostatic potential due to point charges is the solution of Poisson equation (thought I've never seen the proof - any reference?). 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?). 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?). 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; apbs-users@... >> *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:ganuongphap@...] >>> *Sent:* Tuesday, June 03, 2014 2:47 AM >>> *To:* apbs-users@... >>> *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; apbs-users@... >> *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:ganuongphap@...] >>> *Sent:* Tuesday, June 03, 2014 2:47 AM >>> *To:* apbs-users@... >>> *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. >>> >> >> > > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Ooker - 2014-06-04 14:54:54 Attachments: Message as HTML ```> 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. > Another point: as far as I remember, Coulomb electrostatic potential due to point charges is the solution of Poisson equation (thought I've never seen the proof - any reference?). Well, if you see the equation, it is exactly that. The purpose of Poisson equation is for finding the potential. >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? >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; apbs-users@... > 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:ganuongphap@...] > Sent: Tuesday, June 03, 2014 2:47 AM > To: apbs-users@... > 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; apbs-users@... > 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:ganuongphap@...] > Sent: Tuesday, June 03, 2014 2:47 AM > To: apbs-users@... > 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. > > > > > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Radovan Dvorsky - 2014-06-04 17:36:52 Attachments: Message as HTML ```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 interactions between molecules inionic solutions ; - 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; apbs-users@... > > > 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:ganuongphap@... > ] > > Sent: Tuesday, June 03, 2014 2:47 AM > > To: apbs-users@... > > > 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; apbs-users@... > > > 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:ganuongphap@... > ] > > Sent: Tuesday, June 03, 2014 2:47 AM > > To: apbs-users@... > > > 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. > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > Learn Graph Databases - Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases and > their > > applications. Written by three acclaimed leaders in the field, > > this first edition is now available. Download your free book today! > > http://p.sf.net/sfu/NeoTech > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apbs-users@... > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > ```
 Re: [apbs-users] Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file? From: Ooker - 2014-06-05 01:32:52 Attachments: Message as HTML ```> @ 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?) Ahh, did you mean that: "at zero concentration of ions, PBE becomes Poisson equation"? Well, I think so. > @ In my opinion - that describeselectrostatic > interactions between > molecules inionic solutions > ; - 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?) I agree that the PBE describes the potential of the protein and other ions, and that potential is depended on the permittivity of the media. However, I don't think that and the Wiki's definition conflict. >> >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.... Well, I don't think there is any problem here. Ooker. ```