AMBER Archive (2007)

Subject: AMBER: Thermodynamic Integration for a CHARGED molecule

From: ming hui (yongminghui_at_gmail.com)
Date: Fri Aug 17 2007 - 04:12:38 CDT

Dear all,

I am currently trying to calculate the free energy of binding of a molecule
of Tris with charge=+1,
with the double decoupling method that involves thermodynamic integration.

When I am decoupling the electrostatic interactions of Tris from clambda=0
to clambda = 1,
how do I keep the system neutral?
(since at the beginning I would need one Cl- ion, and at the end no ion
would be needed)

I would really appreciate any advice on this matter!
Thank you.

Regards,
Ming Hui

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