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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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