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
