Dear all Gmx users n developers, I am a beginner of Gromacs user, hence I am quite new to the system..May i know how to develop the missing dihedral parameter? Any guide n comments will be appreciated. Thanks
--- On Fri, 7/4/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] segmentation fault during MD > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > <[email protected]> > Date: Friday, July 4, 2008, 6:41 PM > hhhh huan wrote: > > Dear gmx users and developers. > > > > I was running a simulation with 5 ns. But it stated > "segmentation fault" at time around 1 ns, and the > simulation was stopped. > > > > By the way, i faced 2 warning during running the > Grompp, it stated there:" warning 1 No default > Ryckaert-Bell types, using zeroes" > > File 'p1.top' , line 209 > > warning 2 No default Ryckaert-Bell types, using > zeroes" > > File 'p1.top' , line 210 > > > > > > i know that thses are the missing force field > parameter at the indicated line,but i keep on running the > simulation and the segmentation fault appeared because i > cant find any force field that is suitable for the > particular atoms. However, I manage to finish the energy > minimization. > > > > > > So, is it the segmentation fault has anything to do > with the 2 warning? or there is any other way to solve my > problems? > > > > > > You need to find/develop parameters for the missing > dihedral > parameters. Running a simulation with missing information > will likely > lead to inaccurate/questionable results. > > As for whether that directly lead to the segmentation > fault, that's > difficult to diagnose, but I would start by getting the > missing > parameters to eliminate it as a possibility. > > -Justin > > > Thanks a lot > > > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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 [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php

