[gmx-users] Re: The largest charge group contains 1000 atoms

Justin Lemkul jalemkul at vt.edu
Wed Oct 3 13:22:30 CEST 2012

On 10/3/12 1:40 AM, Ashok Kumar Das wrote:
> Dear Dr. Justin A. Lemkul,
> I am Dr. Ashok Kumar Das from IHPC, Singapore.
> I am a new GROMACS learner.
> The system I wish to simulate contains 125 polymer
> chains, each chain containing 8 beads (CH3 and CH2 groups).
> These beads do not have any charge on them.
> I mention charge = 0.0 in the *.gro file.

There are no charges in .gro files.  If you have manipulated the .gro file by 
adding new information, you will break its format.

> In the *.gro file, the chains are arranged sequentially,
> making a total of 1000 atoms. I use atom names as
> 'CH3' and 'CH2', with zero charge.
> However, on running 'grompp' to make the *.tpr file,
> I get the error message:
> "The largest charge group contains 1000 atoms.
> The maximum is 32."
> Kindly guide us how to correct the problem.

I think the error message speaks for itself.  You have every atom of your system 
in a single charge group.  You don't have any charges on the atoms, but the size 
of the charge group will have negative implications for neighbor searching. 
Consult the manual about what a charge group is and how it is used.  Normal 
charge groups are between 1-4 atoms in size, depending on the nature of the group.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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