Fwd: FEP protein-ligand tutorial 2017 unclear section

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 04 2018 - 00:39:24 CDT

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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