[AMBER] Does the PBSA Calculation Include the Neutralizing Plasma£¿

From: ½ªÑô <jy1990217.126.com>
Date: Wed, 9 Mar 2016 11:27:01 +0800 (CST)

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
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