[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround?

Michael Daily mdaily.work at gmail.com
Thu Mar 10 20:14:40 CET 2016


I am trying to do a solvation free energy calculation on a small peptide in
gromacs 5.0.  The peptide is in an extended conformation about 2.5 nm long,
and I use position restraints on the heavy atoms to keep it in this
conformation.  Due to the nature of the calculation I set
"couple_intramol=no" in the mdp file (attached for lambda=0).

However, due to the way couple_intramol is implemented in gromacs
(long-range exclusions), the longest bonded interaction is as long as the
molecule, leading to a minimum cell size of over 3 nm, which makes domain
decomposition all but impossible (see the attached log file).  Is there a
way to limit long-range exclusions and still get reasonable charging free
energies? I have a few ideas but would like some opinions on whether they
are physically sound:

1) change "couple_intramol" to yes and generate intramolecular exclusions
manually with some cutoff.  Since rlist/rcoulomb/rvdw are 1.2 nm for this
simulation, I might use a cutoff of 1.5 to provide a buffer.
2) Use "energygrp-excl = Protein Protein" to turn off nonbonded
interactions within the peptide.  The only problem with this is it forces
the use of group instead of Verlet cutoff scheme which seems to slow
3) Revert to Gromacs 4.7 and use particle decomposition

The log file from my (attempted) simulation with these parameters is also


Michael D. Daily
Research Scientist, Biochemistry and Molecular Biology
University of Texas Medical Branch at Galveston

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