Re: [AMBER] values of f in Thermodynamic Integration

From: Ying-Chieh Sun <>
Date: Fri, 25 Jul 2014 10:50:01 +0800

-----Original Message-----
From: Sun []
Sent: Friday, July 25, 2014 10:25 AM
Subject: [AMBER] values of f in Thermodynamic Integration

Dear all,
In Thermodynamic Integration calculations, several MD simulations with
different f (lambda) values will be performed, for example, for a 5-point
TI calculation , the values of f 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 f 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 f=0,1^?
- - I think you don't always need to use Gaussian integration. When you use
other integration schemes, they are good then.
- - Best.
- - Ying-chieh

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 !

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