Hi Prof Case,
I am using 10 lambda windows for hit and trial, but there is a endpoint catastrophe which I am not sure of how to tackle…
Will setting up TI runs at lambda values 1 and 0 be problematic? That is at lambda values 1 and 0, will that cause issues?
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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Friday, October 25, 2019 11:59:58 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] TI on gpus
On Fri, Oct 25, 2019, Debarati DasGupta wrote:
>I did run a set of TI calculations and I have got 10 windows ( clambda
>varies from 0 to 1 , in increments of 0.1)
>
>Amber tutorial does not explain to how to analyze the output file.
Please read Section 21.1 ("Thermodynamic Integration") in the Reference
Manual, and especially section 21.1.4. You will need to do a numerical
integration of <dV/dl> with lambda going from 0 to 1. Try Simpson's
rule, although your desciption above is a little unclear: do you have 10
windows, or 11?
....dac
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Received on Fri Oct 25 2019 - 13:00:02 PDT
