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

XAvier Periole x.periole at rug.nl
Sun Jan 11 00:31:42 CET 2015

Could be a water molecule broken at the box limits. Try to rebuild the water molecules before minimizing. Trjconv -pbc mol -f in.gro -o out.gro would do it. 

> On Jan 11, 2015, at 00:17, Jonathan Saboury <jsabou1 at gmail.com> wrote:
> 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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