[gmx-users] how to simulate a line charge

Amit Choubey kgp.amit at gmail.com
Sat Aug 13 06:07:44 CEST 2011

On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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.

Not even if i use a 3 body angle term with equilibrium angle = 180? If not
then why ?

>  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
>> website at http://www.gromacs.org/**Documentation/Errors<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.

Thanks for the pointer and the awareness remark. But since this is a model
system and for the physical problem i am trying to deal with its alright if
the atoms within the line charge do not interact via non-bonded potentials.

> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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