Quoting Baofu Qiao <qia...@gmail.com>: > > If you are really sure about the topology, the problem is the initial > structure. Try to use PackMol to build it. >
For simple molecules in water, there is no need for a complicated program like packmol. Such a configuration can easily be built in Gromacs. I have yet to see any evidence of an error. From the original post, it seems that EM failed to start at all. -Justin > On 11/26/2010 11:42 AM, Olga Ivchenko wrote: > > I tried today to run minimization in vacuum for my small molecules. This > has > > the same error. > > > > 2010/11/26 Baofu Qiao <qia...@gmail.com> > > > > > >> Have you run the energy minimization (or further simulation to optimize > >> the structure and test the FF) on the small molecule before you added it > >> into water? > >> > >> On 11/26/2010 11:26 AM, Olga Ivchenko wrote: > >> > >>> Dear gromacs users, > >>> > >>> I am trying to run simulations for small molecules in water. Topology > >>> > >> files > >> > >>> I created by my self for charm ff. When I am trying to start energy > >>> minimization I got an error: > >>> > >>> > >>> Steepest Descents: > >>> > >>> Tolerance (Fmax) = 1.00000e+00 > >>> > >>> Number of steps = 1000 > >>> > >>> > >>> That's means my system is exploding. Please can you advice me on this, > >>> > >> what > >> > >>> I need to check. > >>> > >>> best, > >>> > >>> Olga > >>> > >>> > >>> > >> > >> -- > >> ************************************ > >> Dr. Baofu Qiao > >> Institute for Computational Physics > >> Universit�t Stuttgart > >> Pfaffenwaldring 27 > >> 70569 Stuttgart > >> > >> Tel: +49(0)711 68563607 > >> Fax: +49(0)711 68563658 > >> > >> -- > >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists > >> > >> > > > > > -- > ************************************ > Dr. Baofu Qiao > Institute for Computational Physics > Universit�t Stuttgart > Pfaffenwaldring 27 > 70569 Stuttgart > > Tel: +49(0)711 68563607 > Fax: +49(0)711 68563658 > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
