[gmx-users] Energy minimization error
hmkvsri at gmail.com
Fri Apr 15 18:47:44 CEST 2011
On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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