Hi Thakur,
The tolerance needed to achieve a converged result is
system-dependent. Basically, what you need to do is what you have
done: keep lowering the tolerance until there's no variation in the
free energy.
As I said, this is system-dependent, but for general complex
biomolecules, 0.01 is always too large. I've had to go as low 10^-6 /
10^-7 in several occasions.
Best,
Diego SP
"Thakur, Abhishek" <axt651.miami.edu> escribió:
> ________________________________
> From: Thakur, Abhishek <axt651.miami.edu>
> Sent: Thursday, October 12, 2017 10:02 AM
> To: amber.ambermd.org
> Subject: [AMBER] Wham analysis
>
> Hi everyone,
>
>
> I have some question regarding Wham analysis
>
>
> As per amber tutorial, I have multiplied my force constant with 2
> for wham analysis.
>
>
> But while doing WHAM analysis
>
>
> wham 1.1 3.6 32 0.01 300 0 meta.dat resul.txt
>
>
> 0.01 is the tolerance for reconstructing the PMF in Kcal
>
>
> If I change the value from 0.01 to 0.0001 and keep on changing until
> and unless my result stop changing, it seems that my result has
> changed from 18Kcal/mol to around 50Kcal/mol.
>
> I am confused why energy barrier has changed so much.
> Can anyone suggest me that I can move ahead with results obtained
> with 0.01 kcal or not
>
>
>
>
> Thanking you,
>
> -AT
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Received on Sat Oct 14 2017 - 13:00:03 PDT
