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.scoc...@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:vvcha...@gmail.com] > Inviato: giovedì, 30. luglio 2009 12:42 > A: gmx-users@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: cha...@univer.kharkov.ua,vvcha...@gmail.com > skype: vvchaban, cell.: +38-097-8259698 > http://www-rmn.univer.kharkov.ua/chaban.html > =================================== > !!! Looking for a postdoctoral position !!! > =================================== > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
