Dear Amber users,
I am now using the pbsa module to calculate the reaction field energy of a small charged molecule.
My question is about the neutralization of my system.
The PB solver designed for the periodic boundary condition (bcopt = 10) requires a charge neutral system.
As I know, AMBER may add a uniform neutralizing plasma to a charge unneutral system when using the PME approach.
I want to know if the pbsa module may also add the neutralizing plasma to my charge unneutral system under the periodic boundary condition.
If not, how can I manually add the uniform neutralizing plasma to the charge density (like the form:
new density = old density - Q/V, where Q is the net charge of the molecule and V is the volume of the whole grid box)?
Thanks to all in advance for my question.
Best wishes
Yang Jiang
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Received on Tue Mar 08 2016 - 19:30:04 PST
