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
