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

Justin Lemkul jalemkul at vt.edu
Sun Jan 11 16:00:34 CET 2015

On 1/10/15 7:36 PM, Jonathan Saboury 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

The coordinates here are total trash.  The "UNK" molecule (biotin?) is 
completely nonphysical, and as you note, you have H atoms scattered all around. 
  This suggests a problem with the original system.gro, probably some formatting 
error in the .gro file that caused the coordinates to be misaligned, perhaps 
when adding the ligand coordinates?  If that's the case, no trjconv magic will 
save you; you have to use the proper format.  grompp complaining about the 
charge group size is a strong indication that something is fundamentally wrong 
with the contents of the system.


> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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