[gmx-users] how to simulate a line charge

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 13 05:55:40 CEST 2011

Amit Choubey wrote:
> Hi all,
> I am trying to do a calculation on an artificial line charge in vacuum. 
> The line charge has 267 atoms and each atom has a 1e charge. The atoms 
> are bonded by a bond term and an angle term. I defined the required itp 

If you're trying to keep the atoms in a line, the system will not be stable. 
Angles of 180 degrees routinely crash.

> files and top file. When i issue
> grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp
> I get the following error message.
> Program grompp_jpt, VERSION 4.5.3
> Source code file: grompp.c, line: 175
> Fatal error:
> The largest charge group contains 267 atoms. The maximum is 32.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> What should i try to do to circumvent this error.

The maximum charge group size is defined in the include/types/nblist.h header. 
You can alter the value there, which will get around the error, but consider 
whether or not this is even a good physical model.  If all atoms are in the same 
charge group, there are no electrostatic interactions between these atoms since 
neighbor searching is done and short-range energies are calculated based on 
inter-charge group distances.  I have no idea how to properly simulate a line of 
positively-charged particles, but be aware.



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


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