[gmx-users] Counter-ion problem

Jang Seokyoung yerca at sunni.cnu.ac.kr
Mon Jul 1 06:44:17 CEST 2002


I need your advice.

I have -4.00 charge molecule and +1 charge molecule.

I want to run normal M.D with this two Molecules in one system.

but, I don't konw whether using Counter-ion or not.

I think three cases.

 1. using Counter ion ( 4 Na+ and 1 Cl- )
 2. not using Counter ion ( Total charge -3.00 )

 3. Adding Hydrogen atom ( to make -OH instead of O-1 , and NH2 instead of NH+1 )

Which is more favorate and more stable ? 
please, your advice.
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