[gmx-users] Linear CG beads, grompp doesn't work
jalemkul at vt.edu
Wed Jan 2 04:38:14 CET 2013
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:
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,
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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