Ok thanks On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul <jalem...@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 > 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. > > -Justin > > > Thanking you >> With regards >> kavya >> >> > -- > ======================================== > > 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 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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