On 1/1/13 10:33 PM, Xu Dong Huang wrote:
Dear advanced gromac users,
I am trying to simulate a long linear chain of polymer using CG beads. (about
200 beads), all with same type charge interactions. (examples shown:) I read on
previous gromacs mailing list that linear systems with same charges make the
system unstable? But is there anyway to go around that?
It's the angles that make the system unstable. One can use virtual sites to get
around the issue. There is a trivial example in a tutorial I wrote:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html
The bigger question is whether or not the angles in the molecule impose
linearity, or whether the initial configuration is simply a line of particles
that may deviate according to angle and dihedral potentials. You haven't shown
the [angles] or [dihedrals] directives, so it's not clear what you're intending,
exactly.
[atoms]
1 P3 O1 mon 1 0.00
2 P3 O1 mon 2 0.00
3 P3 O1 mon 3 0.00
4 P3 O1 mon 4 0.00
5 P3 O1 mon 5 0.00
6 P3 O1 mon 6 0.00
7 P3 O1 mon 7 0.00
8 P3 O1 mon 8 0.00
9 P3 O1 mon 9 0.00
…….
[ bonds ]
1 2 1 0.43 17000
2 3 1 0.43 17000
3 4 1 0.43 17000
4 5 1 0.43 17000
……
However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr
-it returns the error of:
Fatal error:
The largest charge group contains 200 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Please let me know if there is a way to go around that. Thank you.
Do as the error message says and put fewer than 32 atoms in each charge group.
The size of the charge group has implications for neighbor searching if using a
group-based cutoff scheme.
-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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