VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 04 2018 - 00:37:18 CDT

Perhaps this question about "FEP with Intermediary Segmants" has passed
unnoticed.
thanks
for paying attention to

fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Apr 26, 2018 at 5:20 PM
Subject: FEP with intermediary segments
To: NAMD <namd-l_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>

Hello:
For the Unbound ligand, in the frame of ligand-receptor FEP, I carried out,
formally successfully, the following segment of the Hamiltonian steep region

frwd 0.00 0.20 0.05
back 0.20 0.00 -0.05

using preeq 1ns, FEP 6ns, and I/O outputs 2000

Because of scalability problems, I have now divided the remaining region in
two sectors.
For the 0.2-0.6 sector:

frwd 0.20 0.60 0.1
back 0.60 0.20 -0.1

ParseFEP gave only a log file with tables for
Free energy perturbation
Inaccuracy
perturbation theory

NO graphic outputs and no useful warning

Was the setting up of the FEP incorrect, or intermediary sectors can not be
used?

Thanks for advice
francesco pietra