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## [apbs-users] Overestimation of electrostatic potential in vacuum?

 [apbs-users] Overestimation of electrostatic potential in vacuum? From: Reisser, Sabine (IOC) - 2013-01-21 15:41:43 ```Dear APBS users and developers, if I calculate the electrostatic potential at a distance of 1 A from a point charge with one e in vacuum via E_pot = 1/(4*Pi*Eps_0*r)*q I get a value of 14.4V. I would expect that this would far be the maximum value of E_pot that I can get on a molecular surface. When I do calculations on the solvent accessible surface of an amphiphilic peptide in vacuum (eps_r=1), however, I get maximum values of 20 000 kT/e, being 520 V . Is there some known overestimation for low dielectric constants? Thanks for reading and with best regards, Sabine ```

 [apbs-users] Overestimation of electrostatic potential in vacuum? From: Reisser, Sabine (IOC) - 2013-01-21 15:41:43 ```Dear APBS users and developers, if I calculate the electrostatic potential at a distance of 1 A from a point charge with one e in vacuum via E_pot = 1/(4*Pi*Eps_0*r)*q I get a value of 14.4V. I would expect that this would far be the maximum value of E_pot that I can get on a molecular surface. When I do calculations on the solvent accessible surface of an amphiphilic peptide in vacuum (eps_r=1), however, I get maximum values of 20 000 kT/e, being 520 V . Is there some known overestimation for low dielectric constants? Thanks for reading and with best regards, Sabine ```
 Re: [apbs-users] Overestimation of electrostatic potential in vacuum? From: Baker, Nathan - 2013-01-21 17:17:31 ```Hello -- What is the resolution (spacing) of the grid you are using for this test calculation? Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Phone: +1-509-375-3997 http://nabaker.me On 1/21/13 7:41 AM, "Reisser, Sabine (IOC)" wrote: >Dear APBS users and developers, > >if I calculate the electrostatic potential at a distance of 1 A from a >point charge with one e in vacuum via E_pot = 1/(4*Pi*Eps_0*r)*q I get a >value of 14.4V. I would expect that this would far be the maximum value >of E_pot that I can get on a molecular surface. > >When I do calculations on the solvent accessible surface of an >amphiphilic peptide in vacuum (eps_r=1), however, I get maximum values of >20 000 kT/e, being 520 V . > >Is there some known overestimation for low dielectric constants? > >Thanks for reading and >with best regards, > >Sabine >-------------------------------------------------------------------------- >---- >Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, >MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current >with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft >MVPs and experts. SALE \$99.99 this month only -- learn more at: >http://p.sf.net/sfu/learnmore_122412 >_______________________________________________ >apbs-users mailing list >apbs-users@... >https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] Overestimation of electrostatic potential in vacuum? From: Sabine Reisser - 2013-01-21 18:07:54 Attachments: apbs_die1_noions.in ```Hi Nathan, I'm using the default parameters from the use with VMD, only changed sdie. I used the multivalue tool of APBS to get the actual surface values. In fact, I think I just found out what the problem was. I still had ions in my calculations. When I remove them, I get values of maximum 300 kT/e = 7.8 V. This is well below my calculated maximum. I'm attaching the parameters which produced a (seemingly) correct result. Cheers Sabine On 01/21/2013 06:17 PM, Baker, Nathan wrote: > Hello -- > > What is the resolution (spacing) of the grid you are using for this test > calculation? > > Thanks, > > __________________________________________________ > Nathan Baker > > Pacific Northwest National Laboratory > Phone: +1-509-375-3997 > http://nabaker.me > > > > > > On 1/21/13 7:41 AM, "Reisser, Sabine (IOC)" wrote: > >> Dear APBS users and developers, >> >> if I calculate the electrostatic potential at a distance of 1 A from a >> point charge with one e in vacuum via E_pot = 1/(4*Pi*Eps_0*r)*q I get a >> value of 14.4V. I would expect that this would far be the maximum value >> of E_pot that I can get on a molecular surface. >> >> When I do calculations on the solvent accessible surface of an >> amphiphilic peptide in vacuum (eps_r=1), however, I get maximum values of >> 20 000 kT/e, being 520 V . >> >> Is there some known overestimation for low dielectric constants? >> >> Thanks for reading and >> with best regards, >> >> Sabine >> -------------------------------------------------------------------------- >> ---- >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, >> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current >> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft >> MVPs and experts. SALE \$99.99 this month only -- learn more at: >> http://p.sf.net/sfu/learnmore_122412 >> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] Overestimation of electrostatic potential in vacuum? From: Baker, Nathan - 2013-01-22 00:43:22 ```Good news; I'm glad you figured it out! Decreasing the grid spacing by increasing"dime" or decreasing "fglen" should further improve agreement. Thanks, Nathan ----- Original Message ----- From: Sabine Reisser [mailto:sabine.reisser@...] Sent: Monday, January 21, 2013 10:07 AM To: Baker, Nathan Cc: apbs-users@... Subject: Re: [apbs-users] Overestimation of electrostatic potential in vacuum? Hi Nathan, I'm using the default parameters from the use with VMD, only changed sdie. I used the multivalue tool of APBS to get the actual surface values. In fact, I think I just found out what the problem was. I still had ions in my calculations. When I remove them, I get values of maximum 300 kT/e = 7.8 V. This is well below my calculated maximum. I'm attaching the parameters which produced a (seemingly) correct result. Cheers Sabine On 01/21/2013 06:17 PM, Baker, Nathan wrote: > Hello -- > > What is the resolution (spacing) of the grid you are using for this test > calculation? > > Thanks, > > __________________________________________________ > Nathan Baker > > Pacific Northwest National Laboratory > Phone: +1-509-375-3997 > http://nabaker.me > > > > > > On 1/21/13 7:41 AM, "Reisser, Sabine (IOC)" wrote: > >> Dear APBS users and developers, >> >> if I calculate the electrostatic potential at a distance of 1 A from a >> point charge with one e in vacuum via E_pot = 1/(4*Pi*Eps_0*r)*q I get a >> value of 14.4V. I would expect that this would far be the maximum value >> of E_pot that I can get on a molecular surface. >> >> When I do calculations on the solvent accessible surface of an >> amphiphilic peptide in vacuum (eps_r=1), however, I get maximum values of >> 20 000 kT/e, being 520 V . >> >> Is there some known overestimation for low dielectric constants? >> >> Thanks for reading and >> with best regards, >> >> Sabine >> -------------------------------------------------------------------------- >> ---- >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, >> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current >> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft >> MVPs and experts. SALE \$99.99 this month only -- learn more at: >> http://p.sf.net/sfu/learnmore_122412 >> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> https://lists.sourceforge.net/lists/listinfo/apbs-users ```