[gmx-users] help on Graphene Nano Sheets

[marcello cammarata]

yes, i used the Minoia tutorial,
i use a cnt_oplsaa at the first attempt, and forward i copied and modify 
the standard oplsaa folder. with both of them i have the same trouble.

  The inizial graphene layer was created using*VMD modelling toolbox*, 
that was a .pdb file, i convert it in .gro file using *editconf *command.
i open the gro file using Avogadro, and it is still a layer. But in the 
gro file the connections are loose.
here  i report the firt 5 rows of the graphene.gro file.

UNNAMED
   112
     1GRA      C    1   0.000   0.000   0.000
     2GRA      C    2  -0.123   0.071   0.000
     3GRA      C    3  -0.123   0.213   0.000
     4GRA      C    4   0.000   0.284   0.000
     5GRA      C    5   0.246   0.000   0.000

thanks

Il 22/04/2015 19:46, Alex ha scritto:
> Hello,
>
> The forcefields for CNT and graphene are identical (for the purpose of
> this discussion). Two questions:
>
> 1. Where did you get the initial graphene structure?
> 2. Are there any CONECT statements in it?
>
> I assume you used Andrea Minoia's guide and the contents of your
> cnt2_oplsaa.ff directory correspond to what he's got.
>
> Alex
>
> MC> Hi,
> MC> i am trying to model a Graphene nano sheet GNS on Gromacs-
> MC> I follow the advices about the nanotubes presented in the help site.
>
> MC> _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_
>
> MC> I run this command to greate the topology:
> MC> _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_
>
> MC> I got this error message:
>
> MC> GROMACS:      gmx x2top, VERSION 5.0.4
> MC> Executable:   /usr/local/gromacs/bin/gmx
> MC> Library dir:  /usr/local/gromacs/share/gromacs/top
> MC> Command line:
> MC>    g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa
>
> MC> Opening force field file
> MC> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t
> MC> Opening force field file
> MC> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t
> MC> There are 12 name to type translations in file cnt2_oplsaa.ff
> MC> Generating bonds from distances...
> MC> atom 112
> MC> There are 1 different atom types in your sample
> MC> Generating angles and dihedrals from bonds...
> MC> segmentazion fault (core dump created)
>
> MC> Someone can help me on this?
> MC> The graphene force field for nanolayer is the same for nanotube? There
> MC> is something that i have to change?
>
> MC> bests
>
> MC> --
> MC> Marcello Cammarata, Ph.D.
> MC> 3208790796
>
>
>
>

-- 
Marcello Cammarata, Ph.D.
3208790796