Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :)
On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/22/15 7:22 PM, marcello cammarata wrote: > >> yes, i used the Minoia tutorial, >> i use a cnt_oplsaa at the first attempt, and forward i copied and modify >> the >> standard oplsaa folder. with both of them i have the same trouble. >> >> > The seg fault will always occur with version 5.0.4; there is a bug we > discovered a few weeks back: > > http://redmine.gromacs.org/issues/1711 > > You'll need to use an older version (pre-5.0) for x2top to work properly > (or patch the code and upload a fix to solve the bug :). > > The inizial graphene layer was created using*VMD modelling toolbox*, >> that was >> a .pdb file, i convert it in .gro file using *editconf *command. >> i open the gro file using Avogadro, and it is still a layer. But in the >> gro file >> the connections are loose. >> > > CONECT entries in PDB files are rarely (never?) used in GROMACS. They are > totally irrelevant for the purpose of x2top. > > -Justin > > > here i report the firt 5 rows of the graphene.gro file. >> >> UNNAMED >> 112 >> 1GRA C 1 0.000 0.000 0.000 >> 2GRA C 2 -0.123 0.071 0.000 >> 3GRA C 3 -0.123 0.213 0.000 >> 4GRA C 4 0.000 0.284 0.000 >> 5GRA C 5 0.246 0.000 0.000 >> >> thanks >> >> Il 22/04/2015 19:46, Alex ha scritto: >> >>> Hello, >>> >>> The forcefields for CNT and graphene are identical (for the purpose of >>> this discussion). Two questions: >>> >>> 1. Where did you get the initial graphene structure? >>> 2. Are there any CONECT statements in it? >>> >>> I assume you used Andrea Minoia's guide and the contents of your >>> cnt2_oplsaa.ff directory correspond to what he's got. >>> >>> Alex >>> >>> MC> Hi, >>> MC> i am trying to model a Graphene nano sheet GNS on Gromacs- >>> MC> I follow the advices about the nanotubes presented in the help site. >>> >>> MC> _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ >>> >>> MC> I run this command to greate the topology: >>> MC> _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ >>> >>> MC> I got this error message: >>> >>> MC> GROMACS: gmx x2top, VERSION 5.0.4 >>> MC> Executable: /usr/local/gromacs/bin/gmx >>> MC> Library dir: /usr/local/gromacs/share/gromacs/top >>> MC> Command line: >>> MC> g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa >>> >>> MC> Opening force field file >>> MC> >>> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t >>> MC> Opening force field file >>> MC> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t >>> MC> There are 12 name to type translations in file cnt2_oplsaa.ff >>> MC> Generating bonds from distances... >>> MC> atom 112 >>> MC> There are 1 different atom types in your sample >>> MC> Generating angles and dihedrals from bonds... >>> MC> segmentazion fault (core dump created) >>> >>> MC> Someone can help me on this? >>> MC> The graphene force field for nanolayer is the same for nanotube? >>> There >>> MC> is something that i have to change? >>> >>> MC> bests >>> >>> MC> -- >>> MC> Marcello Cammarata, Ph.D. >>> MC> 3208790796 >>> >>> >>> >>> >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
