[gmx-users] help on Graphene Nano Sheets

Alex nedomacho at gmail.com
Thu Apr 23 19:24:57 CEST 2015

I think we've covered this when I was having the same issue. If you're
trying to simulate a multi-molecule system, then just copy the entire
forcefield .ff folder to your local directory and modify the following


No need to create rtp entries for graphene/nanotubes, so you can
ignore that part of Andrea's tutorial.

Instead of just "C" in his tutorial, come up with a unique label
to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry
for just graphene and convert it to a stand-alone itp by stripping off system
definitions. This is basically opening the top file, removing those
definitions and resaving as *.itp.

After that, you can just use pdb2gmx on the remaining
parts of the system and complete the system topology by hand. I know,
this sounds like a lot of manual tweaking, but this is the paradigm.

Good luck!


MC> I run a graphene nanolayer, usin the below description (from previous mail.
MC> Now i got an other error.  It look like there is a conflict in a force
MC> field system, someone can suggest me how to modify it?
MC> the force field file came from Minoia advices, reported in the web side!
MC> /
MC> //Program grompp, VERSION 4.6.7//
MC> //Source code file: 
MC> /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752//
MC> //
MC> //Fatal error://
MC> //Syntax error - File forcefield.itp, line 31//
MC> //Last line read://
MC> //'1               3               yes             0.5     0.5'//
MC> //Found a second defaults directive./*
MC> *

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