[gmx-users] Linear CG beads, grompp doesn't work

[Justin Lemkul]

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

-- 
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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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