AMBER Archive (2004)

Subject: Re: AMBER: neutrality of charge in AMBER 7

From: David A. Case (
Date: Sat Feb 14 2004 - 14:10:22 CST

On Thu, Feb 12, 2004, Sichun Yang wrote:
> I just wonder how it works in Amber 7 since ischrgd is removed.
> What is the default? Or I should addions manually?

If the charge is very small (essentially just roundoff error away from
zero) then the charges are adjusted slightly to give exactly zero total

Otherwise, a neutralizing plasma is used.

...hope this helps...dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to