[gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

Abhijit Jassem abhijitjassem at gmail.com
Tue Apr 28 14:14:09 CEST 2015

Hi all,

I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (
but without the steps that use the KALP peptide. After I solvate my
membrane, I am trying to run energy minimization, but my steps are moving
much slower than normal and I get the error "Water molecule starting at
atom 109448 can not be settled. Check for bad contacts and/or reduce the
timestep if appropriate.” When I looked this error up, I found that
this suggested that I had a bad starting structure, possibly with atoms
overlapping. Based on this, I assume this error originates when I solvate
my membrane. I am currently using the spc216.gro model. Is this an issue
with my water model or am I doing something else wrong?

Thank you all very much for the help!
Abhijit Jassem
School of Nuclear Engineering
Purdue University
abhijitjassem at gmail.com

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