If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it.
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 >> Universität 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 Universität 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
