Dear David,
Thanks for your kindly response to my question, but I still get a little bit confused that since TI region1 & TI region2 in output represent for system before & after certain perturbation (here TI region1 represents for system with ligand exist while region2 for ligand vanished system), then we should expect that the DV/DL values for these two systems should be differ from each other?
Sincerely,
Songyan Xia
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________________________________
发件人: David A Case <david.case.rutgers.edu>
发送时间: Saturday, March 25, 2023 9:24:22 AM
收件人: Songyan Xia (LHS, 118010341) <songyanxia.link.cuhk.edu.cn>; AMBER Mailing List <amber.ambermd.org>
主题: Re: [AMBER] Thermodynamic Integration DV/DL output
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 - 19:00:02 PDT
