[gmx-users] Re: CNT

[Vitaly V. Chaban]

Hi,

What's the version of your gromacs?

~ Vitaly

>
> 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



-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
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