[gmx-users] segmentation fault during MD and develop parameter
scottiehuan at yahoo.com
Fri Jul 4 15:47:08 CEST 2008
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.
--- On Fri, 7/4/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] segmentation fault during MD
> To: scottiehuan at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> 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
> > 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
> > So, is it the segmentation fault has anything to do
> with the 2 warning? or there is any other way to solve my
> You need to find/develop parameters for the missing
> 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
> parameters to eliminate it as a possibility.
> > Thanks a lot
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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