Re: [AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？

From: Ray Luo <rluo.uci.edu>
Date: Tue, 8 Mar 2016 20:43:23 -0800

Hi Yang,

Yes, with bcopt=10, i.e. pbc, pbsa has to add a neutralizing charge on
the grid if no salt presents in the system. Otherwise, the solver
cannot converge for a charged system. You don't have to do anything to
turn it on ... it's done automatically.

Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Mar 8, 2016 at 7:27 PM, 姜阳 <jy1990217.126.com> wrote:
> 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 - 21:00:05 PST