Re: [Apbs-users] What does total electrostatic energy include?

[Nathan B. <ba...@cc...>]

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

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-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/