[gmx-users] how to keep nanotube cylindrical

[Justin A. Lemkul]

On 5/5/12 10:21 PM, Za Pour wrote:
> Dear Justin
> I appreciate for your reply.I used -maxwarn option because grompp gave me:
> WARNING 1 [file ffbonded.itp, line 2705]:
> Overriding Bond parameters.
>
> old: 0.151 292880 0.151 292880
> new: C C 1 0.1418 478900

OK, that's reasonable.

> I guess I am not using improper in the topology file.my cnt.top file looks like:
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> CNT 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 opls_995 1 UNK C 1 0 12.011 ; qtot 0
> 2 opls_995 1 UNK C 2 0 12.011 ; qtot 0
> 3 opls_996 1 UNK C 3 0 12.011 ; qtot 0
> ......
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
> 1 73 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
> 2 4 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
> .....
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 3 1
> 1 5 1
> 1 71 1
> ......
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 73 1 1.180000e+02 5.622000e+02 1.180000e+02 5.622000e+02
> 1 2 4 1 1.190000e+02 5.622000e+02 1.190000e+02 5.622000e+02
> 4 3 9 1 1.200000e+02 5.622000e+02 1.200000e+02 5.622000e+02
> ........
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> 73 1 2 4 3 1.910000e+02 5.000000e+00 3.000000e+00 1.910000e+02 5.000000e+00
> 3.000000e+00
> 2 1 73 72 3 2.520000e+02 5.000000e+00 3.000000e+00 2.520000e+02 5.000000e+00
> 3.000000e+00
> 1 2 4 3 3 2.240000e+02 5.000000e+00 3.000000e+00 2.240000e+02 5.000000e+00
> 3.000000e+00
> ........
>
>

I'm only guessing about the impropers, but if you don't have any, then the 
carbon rings will deform, which I'm also guessing is part of your problem.

There is a tutorial linked from 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube that may be useful. 
  It also does not appear to use any defined impropers, but perhaps its workflow 
and information will yield better results.

-Justin

-- 
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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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