On Thu, Jul 10, 2003, zhaoxc.puccini.che.pitt.edu wrote:
>
> my solute has a net charge of -8, when I run the simulation, I see AMBER
> does "Forcing neutrality", how was this done? Is this function going
> to affect my system? I WANT my solute to have a net charge of -8 during
> the simulation.
>
You don't say what version you are using, but it sounds like Amber 6 (?).
If so, you should use the "ischrgd" variable to control how the neutral system
is created. I believe you probably want to set ischrgd to 1.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Jul 14 2003 - 16:53:00 PDT
