[gmx-users] help on Graphene Nano Sheets

Alex nedomacho at gmail.com
Wed Apr 22 19:46:37 CEST 2015


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.


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

Best regards,
 Alex                            mailto:nedomacho at gmail.com

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