[AMBER] values of in Thermodynamic Integration

From: Sun <sunbintyy.163.com>
Date: Fri, 25 Jul 2014 10:25:16 +0800 (CST)

Dear all,
In Thermodynamic Integration calculations, several MD simulations with different (lambda) values will be performed, for example, for a 5-point TI calculation , the values of could be 0, 0.1127, 0.5, 0.88729 and 1 ( this is the stratege applied in the paper-- "Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models", JACS 2004, 126, pp4167-4180).However,when equals to 0 or 1, the cooresponding weight used in Gaussian intergration is 0, so these two points actually do not contribute to the final result. My question is : what is the necessity of the two end point simultions ( when =0,1?


ps: In the Amber online tutorial ( tutotial A6), it is said that the end point simulations will be helpful to debug when things go wrong. How to understand this ? What useful informations will the end point simulatons provide when dubug ?


Thanks in advance !


-Sun
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Received on Thu Jul 24 2014 - 19:30:03 PDT
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