AMBER Archive (2007)

Subject: AMBER: Electrostatic Energy in MD Simulation (GB)

From: adelene_at_Stanford.EDU
Date: Thu May 10 2007 - 12:20:32 CDT

Hi, I was looking at my MD output using NAB with GB approximation, and
I'm referring in particular to the "elect." and "genBorn" terms. Based
on my understanding of GB and total electrostatic energy, genBorn
gives the difference in energy between the system in solution and that
in vacuum, while elect gives the coulomb energy calculated in vacuum.
(Please tell me if I am wrong.)

When I run the "Coulomb" calculation in APBS, I do not get the same
energy values as "elect.", which confuses me, because I expect them to
be equal. They have similar trends (if I plot versus time), but
"elect." is positive while that I calculated in APBS is negative.

Does anyone have any insight?

Thanks!

Adelene
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