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