[gmx-users] segmentation fault during MD and develop parameter

[hhhh huan]

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 <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
> 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    gmx-users at gromacs.org
> > 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
> gmx-users-request at gromacs.org.
> > 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
> 
> ========================================