In this paper we used trapezoidal integration to combine the data from all
windows.
Carlos
On Thu, Jan 9, 2020, 3:31 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Dear All,
> In the recent D3R publication by Prof Simmerling, the authors have used
> “For transition steps involving changing the LJ interactions, the λ values
> were set to 0.00922, 0.04794, 0.11505, 0.20634, 0.31608, 0.43738, 0.56262,
> 0.68392, 0.79366 0.88495, 0.95206,0.99078, 0.995 and 0.999. These
> exponentially distributed λ values between 0.00922 and 0.99078, which have
> more λ at regions where dU/dλ changes significantly, as suggested in the
> Amber manual. Based on our experience, the two extra λ values, 0.995 and
> 0.999 can allow the scaled potential function to further approach the true
> end state.”
> (Page 7 of Blinded prediction of protein‐ligand binding affinity using
> Amber thermodynamic integration
> for the 2018 D3R grand challenge 4 Junjie Zou1,2, Chuan Tian1,2, Carlos
> Simmerling1,2,*)
>
> I could not get the corresponding weights used for the last 2 lambda
> values. Does the AMBER manual have the weights for 0.995 and 0.999?
>
> Any help will be useful.
> Thanks
> Regards
>
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Received on Fri Jan 10 2020 - 04:00:02 PST
