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## Re: [apbs-users] sign of the totoal energy

 Re: [apbs-users] sign of the totoal energy From: Baker, Nathan - 2014-03-21 01:47:30 ```Hello -- This difference is simply due to a sign convention on the energy: whether the system is doing work or having work done to it. The fact that the energy differences agree is a good indication that the calculations are consistent and the differences not relevant to most applications. 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/ -----Original Message----- From: Liu, Hanzhong [mailto:HLiu@...] Sent: Wednesday, March 19, 2014 12:06 To: apbs-users@... Subject: [apbs-users] sign of the totoal energy Hi all: I'm using APBS to calculate the polar solvation energy and comparing the result with the one calculated by Delphi. Following are my results. APBS Total energy in solution is 9.9 E+04 KJ/mol, total energy without solution (Coulombic interaction) is 1.0 E+05 KJ/mol, reaction filed energy is -4.1 E+03 KJ/mol Delphi Total energy in solution is -6.6 E+04 KJ/mol. total energy without solution (Coulombic interaction) is -6.2 E+04 KJ/mol, reaction field energy is -4.4 E+03 KJ/mol Comparing these two results, the reaction field energy is pretty close. But in APBS, all the energy is positive. I've also checked outputs of given examples and these energies are all positive. If APBS gives an absolute value then the reaction field energy will be positive. I'm confusing about the sign of the total energy calculated in APBS. ------------------------------------------------------------------------------ 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/13534_NeoTech _______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```

 [apbs-users] sign of the totoal energy From: Liu, Hanzhong - 2014-03-19 19:06:26 ```Hi all: I'm using APBS to calculate the polar solvation energy and comparing the result with the one calculated by Delphi. Following are my results. APBS Total energy in solution is 9.9 E+04 KJ/mol, total energy without solution (Coulombic interaction) is 1.0 E+05 KJ/mol, reaction filed energy is -4.1 E+03 KJ/mol Delphi Total energy in solution is -6.6 E+04 KJ/mol. total energy without solution (Coulombic interaction) is -6.2 E+04 KJ/mol, reaction field energy is -4.4 E+03 KJ/mol Comparing these two results, the reaction field energy is pretty close. But in APBS, all the energy is positive. I've also checked outputs of given examples and these energies are all positive. If APBS gives an absolute value then the reaction field energy will be positive. I'm confusing about the sign of the total energy calculated in APBS. ```
 Re: [apbs-users] sign of the totoal energy From: Baker, Nathan - 2014-03-21 01:47:30 ```Hello -- This difference is simply due to a sign convention on the energy: whether the system is doing work or having work done to it. The fact that the energy differences agree is a good indication that the calculations are consistent and the differences not relevant to most applications. 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/ -----Original Message----- From: Liu, Hanzhong [mailto:HLiu@...] Sent: Wednesday, March 19, 2014 12:06 To: apbs-users@... Subject: [apbs-users] sign of the totoal energy Hi all: I'm using APBS to calculate the polar solvation energy and comparing the result with the one calculated by Delphi. Following are my results. APBS Total energy in solution is 9.9 E+04 KJ/mol, total energy without solution (Coulombic interaction) is 1.0 E+05 KJ/mol, reaction filed energy is -4.1 E+03 KJ/mol Delphi Total energy in solution is -6.6 E+04 KJ/mol. total energy without solution (Coulombic interaction) is -6.2 E+04 KJ/mol, reaction field energy is -4.4 E+03 KJ/mol Comparing these two results, the reaction field energy is pretty close. But in APBS, all the energy is positive. I've also checked outputs of given examples and these energies are all positive. If APBS gives an absolute value then the reaction field energy will be positive. I'm confusing about the sign of the total energy calculated in APBS. ------------------------------------------------------------------------------ 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/13534_NeoTech _______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```