[gmx-users] Re: R: R: CNT

[Vitaly V. Chaban]

Giulio,

Look here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
It seems some ones were missed as migrating from the old site. I will
send you more topologies attached to the next email.

> Moreover, how can I reply directly to a post in the gmx-user list??
You mean, to the particular post in the digest? - Nowise. You may
reply to the whole digest and then edit the subject and the message
body (kill everything except the message you reply to).

Vitaly


On Thu, Jul 30, 2009 at 2:41 PM, Giulio Scocchi<giulio.scocchi at icimsi.ch> wrote:
> Hi Vitaly
>
> Thank you for the tips. Could u please provide me with a link to your topology? I can't find anything on the Gromacs website
>
> Moreover, how can I reply directly to a post in the gmx-user list??
>
> Thank you again!
>
> 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 13:16
> A: Giulio Scocchi; gmx-users at gromacs.org
> Oggetto: Re: R: CNT
>
> You may also find a number of the already generated CNT topologies on
> the gromacs site uploaded by me for different systems containing CNTs
> to see how it should look like.
>
> 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?
>>>


-- 
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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