[gmx-users] Re: CNT

[Vitaly V. Chaban]

Giulio,

I suggest you to try x2top which is spread with gromacs-3.3.1. The
newer versions of x2top are not sain.

Vitaly

On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchi<giulio.scocchi at icimsi.ch> wrote:
> Hi Vitaly
>
> Well, I have downloaded it just a couple of months ago, so I guess it should be 4.0.4
>
> Giulio
>
> ----------------------------------------------------------------------------------------
>
> Giulio Scocchi
>
> iCIMSI - Institute of Computer Integrated Manufacturing for Sustainable Innovation
> www.icimsi.ch
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>
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>
> -----Messaggio originale-----
> Da: Vitaly V. Chaban [mailto:vvchaban at gmail.com]
> Inviato: giovedì, 30. luglio 2009 12:42
> A: gmx-users at gromacs.org
> Cc: Giulio Scocchi
> Oggetto: Re: CNT
>
> 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
> ===================================
> !!! Looking for a postdoctoral position !!!
> ===================================
>



-- 
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
===================================
!!! Looking for a postdoctoral position !!!
===================================