Fwd: ParseFEP for restating FEP

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Mar 23 2018 - 09:00:15 CDT

Otherwise, is it possible to run portions of lambda and then concatenate
the .fepout results?
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Mar 23, 2018 at 8:05 AM
Subject: ParseFEP for restating FEP
To: NAMD <namd-l_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>

May I ask whether there is any plan to make ParseFEP plugin capable of
dealing with restarted FEP.

With receptor-ligand, I found it difficult to get matching free energy for
frwd/back in the 24hr hr allowed on the cluster, taking into account that I
used the max number of nodes for the given size of the system.

Thus, for the UNBOUND simulations, with either SOS or BAR estimator,
Probability Distribution was found to improve from 1 to 4 until good
overlapping, while Free Energy also improves correspondingly, albeit not
doing better than red at -2.50, black at -10.0. By restarting until 100
windows, probably I should have acceptable convergence. Curiously
Enthalpy/Entropy match better (artifact).

I used fifty windows with 50,000 pre-equilibration and 300,000 FEP only (1
node), in order to stay within the 24hr. (a smaller number of windows, even
with much pre-equilibration and FEP, perform worser).
With the ligand-protein I could use a max of 4 nodes (beyond which no
higher speed) with perhaps a max of 10 windows. Bad prospects for

Thanks for your attention

francesco pietra

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