On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > lina wrote: >> >> On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> lina wrote: >>>> >>>> Hi, >>>> >>>> Form the begining to 50000 steps, during EM, all exit in atom 8524, >>>> how do I check it further? I mean, from which parts to examine? >>>> I also switched to double version to run the EM. >>>> >>> Open your structure in a visualization program and look at what it might >>> be >>> clashing with >> >> Thanks, I checked before. >> > > And what did you find? What is the closest atom to the one with the maximal > force? Would its charge cause repulsion? Is it so close that LJ overlap is > causing a problem? In this case, visualization of the problematic structure > is the solution, you just have to take care to identify the source of the > problem. It certainly may not always be obvious.
Thanks, I guess I might make the system so compact. Before in VMD it showed something weird, kind of broken bond, but in PyMOL was fine. Thanks again, > > -Justin > >> >>> -Justin >>> >>>> .... >>>> Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04, >>>> atom= >>>> 8524 >>>> ... >>>> Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04, >>>> atom= >>>> 8524 >>>> ... >>>> Step=50000, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04, >>>> atom= >>>> 8524 >>>> >>>> writing lowest energy coordinates. >>>> >>>> Steepest Descents did not converge to Fmax < 1000 in 50001 steps. >>>> Potential Energy = -2.17266924593509e+05 >>>> Maximum force = 2.89751132744731e+04 on atom 8524 >>>> Norm of force = 2.18622026854678e+02 >>>> >>>> Thanks for any advice, >>>> >>> -- >>> ======================================== >>> >>> 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 >>> >> >> >> > > -- > ======================================== > > 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 > -- Best Regards, lina -- 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
