[gmx-users] Re: CNT

[Vitaly V. Chaban]

Vasilii,

Telling the truth, I don't already remember what was wrong with CNT
topology generation from the coordinate file but I didn't succeed with
any version starting from 3.3.3. So I still keep x2top (3.3.1) for the
CNTs.

There was also several reports in gmx-list that x2top(4.0.X) behaves strangely.

It's interesting for me that you succeeded with graphene. Could you
please share the starting coordinates and the resulting topology?

Vitaly


On Thu, Jul 30, 2009 at 2:20 PM, Vasilii Artyukhov<darth.vasya at gmail.com> wrote:
> Hmm... I've been using the 4.0.4 x2top to create OPLS-AA topologies for,
> e.g., graphane, and it worked more or less right "out of the box", giving
> very convincing results. What's the problem exactly about recent versions of
> x2top? I use the -noparams option to leave everything having to do with
> numbers to grompp. Even periodic boundary conditions for infinite molecules
> seem to be handled correctly...
>
> 2009/7/30 Vitaly V. Chaban <vvchaban at gmail.com>
>>
>> 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
>> > DTI - Department of Innovative Technologies
>> > www.dti.supsi.ch
>> > SUPSI - University of Applied Science of Southern Switzerland
>> > www.supsi.ch
>> >
>> > Via Cantonale - Galleria 2
>> > 6928 Manno
>> > Switzerland
>> > tel: +41 (0)58 666 66 46
>> > fax: +41 (0)58 666 66 20
>> >
>> >
>> > -----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 !!!
>> ===================================
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