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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 04 2018 - 14:47:42 CDT

It seems that the contribution to /\G of restraining the ligand is
accounted for in the .namd files with both /Alchemy:Bound and
/Alchemy:Unbound, and therefore with ParseFEP. Am I wrong?

If I am wrong, is any script to extract /\G from the thermodynamic
integration runs, so as to "add" to the ParseFEP output? Doing that
manually, and necessarily repeatedly for long simulations is a punishment
that perhaps I don't deserve.

thanks
francesco

On Fri, May 4, 2018 at 5:43 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> 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>
> 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>
>
>
> 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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