[gmx-users] help on Graphene Nano Sheets
abhijitchemiitd at gmail.com
Thu Apr 23 20:04:51 CEST 2015
Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
opls_995 C 6 12.01100 0.000 A 3.40000e-01
opls_996 C 6 12.01100 0.000 A 3.40000e-01
opls_997 C 6 12.01100 0.000 A 3.40000e-01
Then in atomname2type.n2t file add the following lines.
C opls_995 0 12.011 2 C 0.142 C 0.142
C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
C opls_997 0 12.011 1 C 0.142
Then use g_x2top. This will work.
On Thu, Apr 23, 2015 at 10:54 PM, Alex <nedomacho at gmail.com> wrote:
> 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
> 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
> 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
> 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:
> 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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