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
