Re: [AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration

From: Jason Swails <>
Date: Wed, 14 Jul 2010 11:18:23 -0400


This limitation on lambda is only for soft core ti. These aren't weights, per se, but rather values of the alchemical parameter lambda. I suppose this can be viewed as the weight of the second hamiltonian... What is important about doing ti calculations is that you can integrate from 0 to 1 with reasonable accuracy...

Hope this helps,

Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
On Jul 14, 2010, at 8:16 AM, sunita gupta <> wrote:
> Hello everyone,
> I have a query regarding weight calculation for different Abscissa in
> Thermodynamic Integration. As, in the manual of Amber10, the maximum of 12
> Abscissa and their corresponding weights are given in the table4.1. Among
> these 12 values two of the values ie. 0.00922 and 0.99078 does not work as
> they lie outside the range of 0.01 < clambda < 0.99.
> My queries are:
> 1. As the weights are calculated according to the 12 abscissa values. will
> it make any difference if we are successfully running only 10 values?/ or
> should we take some other weight values as per 10 lambda values?
> 2. As suggested if, convergence is not enough we can anytime introduce more
> number of lambda values (windows) or extend the runs. I want to know, what
> will be the selection procedure of new lambda values and what will be the
> weight corresponding to those new lambda values?
> Thanks in Advance
> Regards
> -- 
> -- 
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed Jul 14 2010 - 08:30:03 PDT
Custom Search