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.
---------- 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>
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
in the frame of files provided in
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.
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