[gmx-users] Energy minimization error

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 15 18:26:08 CEST 2011

Kavyashree M wrote:
> Dear gromacs users,
> While doing energy minimization for a protein (from pdb), with oplsaa 
> force field
> and tip4p water model, there was an error and em stopped -
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> What is the correction for this?

Build a more reasonable starting structure.  Somewhere you have atomic overlap 
or otherwise unresolvable geometry such that you have atoms flying across the 
system, as the error message indicates (although somewhat obliquely).

The screen/log output from mdrun should print where the high forces are, or 
which atoms are having constraint problems, etc.  Investigate these atoms in 
your starting structure and/or EM trajectory and determine an appropriate 
solution based on what you find.


> Thanking you
> With regards
> kavya


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list