[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

Jonathan Saboury jsabou1 at gmail.com
Sun Jan 11 00:17:28 CET 2015

My system is blowing up during minimization. I'm getting the error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

I looked at "http://www.gromacs.org/Documentation/Terminology/Blowing_Up"
with no solution. I am minimizing the system to prevent blowing up, but it
is blowing up in the energy minimization. Bad starting structure is
unlikely because water is showing unusual bond angles and lengths far from
any biotin or protein atoms (in system.gro+em.xtc files).

I found it unusual that atom names in system.top did not match with
system.gro (as seen in the grompp output).

Second warning is:
WARNING 2 [file em.mdp]:
  The sum of the two largest charge group radii (15.152546) is larger than
  rlist (1.000000)
No idea what that means though.

Any ideas? Thank you!

commands used: http://pastebin.com/raw.php?i=ea4dUNT6
grompp output: http://pastebin.com/raw.php?i=gtHwdhuM
em.mdp (.mdp used for minimization): http://pastebin.com/raw.php?i=sRnEMA5F
system.gro + em.xtc(3.8 MB): http://ge.tt/9E7i1L82/v/0
All files (15 MB): http://ge.tt/8FCb2L82/v/0

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