From: Nathan Baker <baker@cc...>  20070924 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 illdefined. 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/ > _______________________________________________ > apbsusers mailing list > apbsusers@... > https://lists.sourceforge.net/lists/listinfo/apbsusers > >  Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ 