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

[XAvier Periole]

The warning of grompp says you have two charge groups (bound groups from a molecule) at 7 nm, while the cutoff of theses interactions is 1 nm! This most likely reflects a broken molecule … 

Visualising your system indicates it is broken all over the place at the PBC. Make your molecule whole first, then solvate it and minimise it. 

The construction of your system is the problem.

On Jan 11, 2015, at 1:36 AM, Jonathan Saboury <jsabou1 at gmail.com> wrote:

> Not likely Xavier. It isn't a single water acting unusual. It is many
> waters (probably all) and all biotins making odd angles/lengths.
> 
> Nevertheless I tried the suggestion and I am getting different results, but
> not sure if they are good results.
> 
> "vmd rebuilt_system.gro em.xtc" shows the system but now there are
> undertemined white dot coordinates surrounding the system. Another curious
> thing is that no atoms are moving in those 16 frames.
> 
> As you can see in the mdrun output the minimization finishes but:
> --------------
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> --------------
> 
> I read "
> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision"
> and Epot is not at right range.
> 
> Commands used: http://pastebin.com/raw.php?i=YjTDnzUQ
> grompp output: http://pastebin.com/raw.php?i=TLtT8tcF
> mdrun output: http://pastebin.com/raw.php?i=YTa09GVE
> 
> rebuilt_system.gro (481 KB): http://ge.tt/9khqEL82/v/0
> em.xtc(1.4 MB): http://ge.tt/5zI9FL82/v/0
> 
> Thank you!
> 
> On Sat, Jan 10, 2015 at 3:17 PM, 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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