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

[hhhh huan]

Dear all Gmx users n developers,
I am happy and appreciate with all the help n suggestions you all have given to me.

Here is my molecule look likes.:

  C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C
                                    |
                                    O
                                    |
C-C-C-C-C-C=C-(c)-C=C-C-C-C-C-C-C-C-C=O
              

The problem that i faced now is the parameter of the OPLS-AA force field for the carbon atom which is in the bracket . I am now still looking for the solutions for this problem. 
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: [gmx-users] Re: segmentation fault during MD and develop parameter
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Friday, July 4, 2008, 10:13 PM
> hhhh huan wrote:
> > 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
> >
> >   
> 
> No one here is going to be able to help, aside from the
> standard, "Yes, 
> you can do it if you read the original paper for the force
> field you 
> want to use."  If you describe your molecule and what
> the missing 
> parameter is (functional group, etc.), then maybe someone
> will have an 
> insight.
> 
> Otherwise, you're in for some parameterization, which
> is not recommended 
> for the novice user.
> 
> -Justin
> 
> >
> >
> > --- 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
> >>>
> >>>
> >>>
> >>>       
> >>>
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> >>>       
> >> 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
> >>
> >> ========================================
> >>     
> >
> >
> >       
> >
> >   
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
> 
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