[AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change

From: Junjian Miao <junjianmiao.gmail.com>
Date: Wed, 16 Mar 2011 20:58:58 +0800

dear all,

regarding thermodynamic integration, i have a couple of questions, one is can i use it to simulate absolute pka, for example, CH3COOH + H2O -->

CH3COO- + H3O+ ?the tutorial A6 demonstrates how to simulate the relative pka, however no comments about absolute one.

another is, for instance, as for reaction A + B --> AB', where the conformation of B changes significantly, in this case, how to simulate the reaction to get the

absolute free energy?

thank you in advance!

Junjian Miao
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Received on Wed Mar 16 2011 - 06:00:03 PDT
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