On Thu, Mar 23, 2023, Songyan Xia (LHS, 118010341) via AMBER wrote:
>
>I'm trying to use amber20 thermodynamic integration to get absolute binding free energy for a protein-ligand complex.
>I've set input parameters as
>"
>icfe = 1, ifsc = 1, clambda = LAMBDA, scalpha = 0.5, scbeta = 12.0,
>logdvdl = 1,
>ifmbar=1, mbar_states=11, mbar_lambda=0.00, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00,
>timask1 = ':NAP', timask2 = '',
>scmask1 = ':NAP', scmask2 = '',
>"
>in TI section as to get absolute free energy according to amber20 manual.
>However, when I'm checking the mdout files from each lambda window, I
>noticed that the DV/DL value out put for each 1000 steps in TI region1 & TI
>region2 are identical to each other throughout the whole simulation.
This sounds correct to me: the DV/DL values represent differences between
the starting and ending points (lambda = 0 vs lambda = 1). They don't
depend on which region is being reported.
...dac
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Received on Fri Mar 24 2023 - 18:30:03 PDT
