Re: Fwd: FEP protein-ligand tutorial 2017 unclear section

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri May 04 2018 - 10:43:47 CDT

The two files are forward and backward runs of what is essentially TI. It’s been a while since I’ve done it, but I believe you can extract dG/dlambda from the log files and then integrate it.

Best,
JC

> On May 4, 2018, at 1:39 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Perhaps this question about "FEP protein-ligand tutorial 2017 unclear section" has passed unnoticed. Thanks for paying attention to.
> fp
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>>
> Date: Wed, May 2, 2018 at 9:51 PM
> Subject: FEP protein-ligand tutorial 2017 unclear section
> To: NAMD <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
>
>
> Hello:
> With reference to the 2017 "Protein:ligand standard binding free energies: A tutorial for alchemical and geometrical transformations" by Gumbart, Roux, Chipot,it is not clear to me how to deal with the two sections of the archive files
>
> 1) Restraints:Bound
> 2) Restraints:Unbound
>
> in the frame of files provided in
>
> 3) Alchemy:Bound
> 4) Alchemy:Unbound
>
> i.e, how the contribution of restraints in 1) and 2) is evaluated (in particular, why rest-01 and rest-02?) and algebraically added, if at all, to 3) and 4).
>
> I could try to imagine what I am unable to find described in tutorial pdf (otherwise I do not see any README), but a clarification here might avoid taking wrong routes.
>
> thanks
> francesco pietra
>
>

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