[AMBER] CpHMD simulation for non protein residues

From: Rahul Ramesh <raramesh.umich.edu>
Date: Wed, 23 Sep 2015 12:05:46 -0400

Hey Jason
I am trying to make sense of the equation given in " Constant pH MD in
Generalized Born Implicit Solvent" by David Case.
[image: Inline image 1]
I understand that del G elec,ref is calculated from the Thermodynamic
Integration. I am not able to get protonation state change for my system
and I want to know how to find the del G elec which the simulation code
calculates so that I can compare that value with my del G elec,ref and
troubleshoot.

Thank You
Rahul Ramesh


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Received on Wed Sep 23 2015 - 09:30:03 PDT
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