Re: [AMBER] how to deal with the system with negative charge ?

From: Dmitry Mukha <>
Date: Tue, 30 Mar 2010 11:47:57 +0300

2010/3/30 sculiujl <>

> Hi amber users,
> As usual we add ions to make the system neutralized. Now the system have
> seven negative charge, but I want to keep the system with one net negative
> charge .So how to dea with it in tleap? I wonder whether there is anyone
> having the similar experience. Any suggestions are welcome. Thanks a lot!
> _______________________________________________
> AMBER mailing list

As I know, system should be neutral during periodic boundary simulation. You
may place ion far away from solute, or use implicit solvent (water), which
does not need any neutralization.

Best regards,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS of Belarus
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Received on Tue Mar 30 2010 - 02:00:02 PDT
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