[gmx-users] help on Graphene Nano Sheets

[Alex]

You don't need to run x2top on the GRO file, you can apply it directly to
the PDB. It seems like the PDB to GRO conversion destroyed the coordinates
due to poor formatting of the initial coordinates. This has nothing to do
with the forcefields or graphene, you may just have a crappy PDB.

Alex


On Wed, Apr 22, 2015 at 5:22 PM, marcello cammarata <
marcello.cammarata at unipa.it> wrote:

>  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
>
>