[gmx-users] Capped CNT

Robert Johnson bobjohnson1981 at gmail.com
Tue May 13 20:49:23 CEST 2008


Well, the end caps contain a few pentagons so the angle terms for
those atoms would have to change from the normal 120 degrees used for
hexagons. Other than that, I don't think the force field parameters
would have to change. What do you mean by the tube "breaking apart"?
That sounds like you don't have the right connectivity in your
topology file.
Bob


On Fri, May 9, 2008 at 11:21 AM, Christopher Stiles <CS145331 at albany.edu> wrote:
> I am attempting to run a simulation involving a (10,10) CNT that is capped
> on one side. Each time I do this the tube breaks apart in the first few
> steps, so I am thinking that the force fields must be modified from how I
> have them set just for an un-capped CNT. If any one has done this or could
> point me in the correct direction I would be very grateful.
>
>
>
> I have also included a copy of my *.pdb file in case that is the issue.
>
>
>
> Thank you!
>
> ~Christopher Stiles
>
>
>
> P.S. I use the following modifications to the ffgmxbon.itp file:
>
>
>
> #####################################
> [ bondtypes ]
> ; i j func b0 kb
> C C 1 0.14210 478900.
> #####################################
> [ angletypes ]
> ; i j k func th0 cth
> C C C 1 120.000 397.480
> #####################################
> [ dihedraltypes ]
> ; i l func q0 cq
> C C 1 0.000 167.360
> #####################################
>
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