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
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