Hi Les --
This question is probably of more general interest, so I'm going to Cc
The potential is dimensionless; the conversion factor depends on the energy
and charge units you want to use. In particular, the factor "k" (the
Boltzmann constant or gas constant) determines the energy and temperature
units and the "e_c" specifies the charge units.
For example, suppose you want to know the energy (in kJ/mol) of a ligand
with charge +1 (in electrons) at position R given the dimensionless
potential u(r) as calculated at 300 K and written out by APBS. You would
E = z * k * T * u(R)
= (+1) * (8.314E-3 kJ/mol/K) * (300 K) * u(R)
= (2.5 kJ/mol) * u(R)
Hope this helps.
Nathan A. Baker, Assistant Professor
Washington University in St. Louis
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
> -----Original Message-----
> From: Les Ander [mailto:les_ander@...]
> Sent: Wednesday, April 07, 2004 8:40 PM
> To: baker@...
> Subject: units of apbs' electrostatic potential in KT/e
> Dear Nathan,
> thank you for a wonderful software.
> I have a question which i hope you can help me with.
> I am not sure I understand the units of potential.
> The documents say that the units are in KT/e
> but clearly KT can be in many units, for example KT is
> 4.1 in pN.nm at room temperature. So my question is if
> apbs says that
> at a certain location, the electrostatic potential is
> -1.0, what is this value in pN.nm (i.e. pico Newtons.
> nano meters)
> thank you very much for you help
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