apbs-users

 [Apbs-users] What does total electrostatic energy include? From: Bihui Li - 2007-09-21 08:39:06 Attachments: Message as HTML ```Hi all, I'm trying to use APBS to calculate the total interaction energy between a Kinesin head and a section of microtubule. Our approach is to calculate the solvation energy plus coulombic energy of the system, for several nearby positions of the Kinesin relative to the microtubule, e.g. at r = (x,y,z), (x+dx,y,z), (x,y+dy,z), (x,y,z+dz). Then would it be accurate to say that the effective force at r = (x,y,z) is (delta E)/(delta r), where E is the solvation energy plus coulombic energy? In particular, is the entropy of the solvent included in the solvation energy calculation, or does the entropy 'cancel out' because the calculation of solvation energy involves taking the change in energy relative to a reference solvent? Thank you, Bihui ```
 Re: [Apbs-users] What does total electrostatic energy include? From: Nathan Baker - 2007-09-24 16:34:04 ```Hello -- > I'm trying to use APBS to calculate the total interaction energy between a > Kinesin head and a section of microtubule. Our approach is to calculate the > solvation energy plus coulombic energy of the system, for Just to clarify: are you using APBS for the solvation energy and some other program (e.g., the provided `coulomb` program) for the Coulombic energies? > Then would it be accurate to say that the effective force at r = (x,y,z) is > (delta E)/(delta r), where E is the solvation energy plus coulombic energy? Are you referring to the analytic forces returned by APBS or the forces you get by evaluating energies at slightly different positions and subtracting the results? > In particular, is the entropy of the solvent included in the > solvation energy calculation, or does the entropy 'cancel out' because the > calculation of solvation energy involves taking the change in energy > relative to a reference solvent? The notion of "entropy" in polar solvation energy calculations is extremely ill-defined. However, the solvation forces returned by APBS or by your finite differencing will include "entropy" terms that will not be canceled by the homogeneous dielectric reference state calculation. Thanks, Nathan > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```
 Re: [Apbs-users] What does total electrostatic energy include? From: Bihui Li - 2007-09-24 23:36:51 Attachments: Message as HTML ```> Just to clarify: are you using APBS for the solvation energy and some > other program (e.g., the provided `coulomb` program) for the Coulombic > energies? I use APBS for the solvation energy and the 'coulomb.py' script for the Coulombic energies. > Then would it be accurate to say that the effective force at r = (x,y,z) > is > > (delta E)/(delta r), where E is the solvation energy plus coulombic > energy? > > Are you referring to the analytic forces returned by APBS or the > forces you get by evaluating energies at slightly different positions > and subtracting the results? The latter. Thanks, Bihui ```
 Re: [Apbs-users] What does total electrostatic energy include? From: Bihui Li - 2007-09-24 23:43:39 Attachments: Message as HTML ```On 25/09/2007, Bihui Li wrote: > > > > > > Just to clarify: are you using APBS for the solvation energy and some > > other program ( e.g., the provided `coulomb` program) for the Coulombic > > energies? > > > I use APBS for the solvation energy and the 'coulomb.py' script for the > Coulombic energies. > Oops, coulomb is not a Python script; I meant to say that I use the provided 'coulomb' program you are referring to. Bihui ```
 Re: [Apbs-users] What does total electrostatic energy include? From: Nathan Baker - 2007-09-27 11:47:51 ```Hello -- > > Are you referring to the analytic forces returned by APBS or the > > forces you get by evaluating energies at slightly different positions > > and subtracting the results? Why aren't you using the analytic APBS forces? Thanks, Nathan -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```