AMBER Archive (2004)

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

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• In reply to: Sichun Yang: "AMBER: neutrality of charge in AMBER 7"
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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
charge.

Otherwise, a neutralizing plasma is used.

...hope this helps...dac

-- 
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David A. Case                     |  e-mail:      case_at_scripps.edu
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• Next message: susan.costantini_at_unina2.it: "AMBER: minimizating complex-protein with AMBER"
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