[gmx-users] Fwd: FW: PME settings in free energy calculations

Michael Shirts mrshirts at gmail.com
Thu Feb 4 00:56:31 CET 2016

Hi, Dries-

Questions like this are probably best answered on the gmx-users list.
I can't say too much for the Verlet scheme -- I know that it was
relatively recently adapted for free energies, and there may be some
combinations of settings that could give unanticipated results.

Pretty much all of our experience about nonbonded calculations and
free energies is collected in the following paper:
http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used the group
cutoff scheme since that was the only one that was supported in
GROMACS at the time.

Since you haven't sent any files, it's hard to tell what is actually
going on. The one thing that has a tendency to happen with the more
recent update schemes is if you set a potential modifier that is a
switch, but don't set the distance the switch starts at, then it is
automatically set to zero.  Check the mdout.mdp to see if this is

> From: Van Rompaey Dries <Dries.VanRompaey at uantwerpen.be>
Date: Wednesday, February 3, 2016 at 12:34 PM
To: Michael Shirts <michael.shirts at colorado.edu>
Subject: PME settings in free energy calculations

Dear prof. Shirts,

I'm currently trying to figure out the PME settings for a relative
free binding energy simulation I'm working on. I took the parameters
from Matteo Aldeghi's
as a starting point (adapted for the Verlet scheme by scaling the
fourierspacing to 0.08 and setting coulomb = rvdw = 1.0). I then tried
to verify these settings by comparing a single point energy
calculation with these settings and one with very long coulomb cutoffs
as recommended on alchemistry.org.

Unfortunately, I can't seem to get this quite right. I'm getting
differences in the hundreds of kj/mol, leading me to suspect I'm doing
something wrong. I'm calculating the energy values by extracting
CoulombSR and Coul-recip from the energy.xvg files. I've tried
calculating the energy with coulomb cutoffs at 3 nm and 10 nm, but
agreement with the PME results remains rather poor. David Mobley
mentioned you performed extensive research on this topic, and I'm
hoping you could point me in the right direction.

Thanks in advance,


Michael Shirts
Associate Professor
michael.shirts at colorado.edu
Phone: (303) 735-7860
Office: JSCBB D317
Department of Chemical and Biological Engineering
University of Colorado Boulder

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