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

Justin Lemkul jalemkul at vt.edu
Tue Apr 28 19:09:25 CEST 2015

On 4/28/15 8:14 AM, Abhijit Jassem wrote:
> 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 (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
> 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

Well, what's going on around atom 109448?

> 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?

There are plenty of potential problems, unfortunately not enough information to 
go on.  Simply using SPC isn't a problem, but something either in the 
configuration or the force field is an issue.  Rather than building a large 
system (you have over 100,000 atoms), do something small, like the pre-built 
DPPC bilayer that the tutorial uses.  That's a sanity check.  If that minimizes 
and equilibrates well, that means the force field is fine and something is wrong 
with the way you built your larger system.  If you want help with that, you have 
to tell us exactly what you're doing (exact command sequence).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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