## apbs-users

 [Apbs-users] Transition Energies in PB From: - 2006-09-12 21:15:31 ```Hi --- I'm trying to compute the electrostatic energy of a transtion between two conformations of a single structure (A->B) in an ion solution. The interior dielectric will be set to 2 (pdie=2) and solution to 80 (sdie=80). I have two questions: 1) Is the appropriate calculation simply to take the difference between NLPB energies for A and B: \DeltaG(A->B) = B(solv, ion) - A(solv, ion) using identical parameters for box size, grid spacing? I'm a bit worried I haven't accounted for the self-energy terms somewhere. 2) What is the criteria for choosing the appropriate box side/grid spacings? I've computed the energy B(solv, ion) - A(solv, ion) for several different box sizes/grid spacings (0.5, 0.4, 0.3 A spacings) and the answers vary quite a bit. Thanks, Vince ```
 Re: [Apbs-users] Transition Energies in PB From: Nathan Baker - 2006-09-14 10:53:03 ```Hello -- > I'm trying to compute the electrostatic energy of a transtion > between two > conformations of a single > structure (A->B) in an ion solution. The interior dielectric will > be set > to 2 (pdie=2) and solution > to 80 (sdie=80). Sounds reasonable. > 1) Is the appropriate calculation simply to take the difference > between > NLPB energies for A and B: > > \DeltaG(A->B) = B(solv, ion) - A(solv, ion) > > using identical parameters for box size, grid spacing? I'm a bit > worried I > haven't accounted for > the self-energy terms somewhere. If you truly are calculating the *solvation* energies: (inhomogeneous dielectric, nonzero ionic strength energy) - (homogeneous dielectric, zero ionic strength energy) then what you describe should provide the change in solvation energy due to the conformational change. You'll still need to supplement this with the change in Coulombic energy to get the total electrostatic energy change. > 2) What is the criteria for choosing the appropriate box side/grid > spacings? I've computed the > energy B(solv, ion) - A(solv, ion) for several different box sizes/ > grid > spacings (0.5, 0.4, 0.3 A > spacings) and the answers vary quite a bit. What surface definition are you using? The necessary grid spacing can vary based on the type of calculation and the surface definition. For spline-based surfaces, results are usually stable (for all types of calculations) when the grid spacing is approximately equal to or smaller than the spline window. Thanks! -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```
 [Apbs-users] Dipole moment from APBS? From: Andy Purkiss-Trew - 2006-11-30 18:30:44 ```Dear All, Does anyone have a way/script/program for generating the dipole moment of a molecule from the potential (or charge) in an opendx file generated by APBS? Andy Purkiss-Trew -- Cat, n.: Lapwarmer with built-in buzzer. +----------------------------------------------------------------------+ | Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London | | E-mail a.purkiss@... | +----------------------------------------------------------------------+ ```