Thank you, Yes, i did energy minimization to the chromophore alone and it stays stable....
The problem arise when i do the energy minimization to the GFP-chromophore full system. It clearly shows the atoms which is expected to connect the negihbouring residues is flying apart. I am still checking on the bond parameters to see whether i missed something. Regards, Rama On Sat, Nov 13, 2010 at 12:54 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Gerrit Groenhof wrote: >> >> Can you perform a simulation of the chromophore alone? Does that stay >> stable? >> > > In that regard, some of the information on the following page may be useful: > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > -Justin > > -- > ======================================== > > 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-us...@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 > -- -- 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