[gmx-users] CNT

[Giulio Scocchi]

Hello everybody

 

I am a Gromacs beginner and I am trying to simulate an infinite graphene
lattice (see 07.29.09 posts - I don't know how to reply directly to
posts, can someone tell me how to do that?). Mark suggested having a
look at  http://www.gromacs.org/WIKI-import/Carbon_Nanotube . I had
already seen that and I hoped there were some kind of more "direct" way.
Anyway, I tried to follow the procedure explained  in Christopher Stiles
website (http://cs86.com/CNSE/SWNT.htm) just to simulate the nanotube
(graphene will come). I downloaded all the files and (as it was
suggested) typed: 

 

 x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

 

and this is what happened:

 

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/aminoacids.dat

WARNING: masses will be determined based on residue and atom names,

         this can deviate from the real mass of the atom type

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/atommass.dat

Entries in atommass.dat: 178

WARNING: vdwradii will be determined based on residue and atom names,

         this can deviate from the real mass of the atom type

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/vdwradii.dat

Entries in vdwradii.dat: 28

Opening library file /homea/scocchi/GROMACS/share/gromacs/top/dgsolv.dat

Entries in dgsolv.dat: 7

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/electroneg.dat

Entries in electroneg.dat: 71

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/elements.dat

Entries in elements.dat: 218

Looking whether force field files exist

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.rtp

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t

WARNING: all CONECT records are ignored

Opening library file
/homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t

There are 23 name to type translations

Generating bonds from distances...

atom 0

 

... and at this point it gets stuck.

 

Does anyone have a clue about what I am doing wrong? Could it be that
this happens because I am using the most recent version of Gromacs? If
so, what should I modify?

 

Thank you!

 

Giulio 

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090730/39fe8a64/attachment.html>