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

From: sunita gupta <sunita.bio.gmail.com>
Date: Wed, 14 Jul 2010 17:46:05 +0530

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

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Received on Wed Jul 14 2010 - 05:30:04 PDT
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