[gmx-users] Re: segmentation fault during MD and develop parameter
hhhh huan
scottiehuan at yahoo.com
Sat Jul 5 13:10:38 CEST 2008
Dear all gmx users, developers, and Justin,
I have tried the OPLS_136 and this is the force field that caused the 2 warnings during grompp and I had also try the other parameters. I think that should be needed a unique parameter development for this molecule.
So, I am still "headache" about this.
Any guide n comments will be appreciated.
Thank you
--- On Sat, 7/5/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: segmentation fault during MD and develop parameter
> To: scottiehuan at yahoo.com
> Date: Saturday, July 5, 2008, 6:38 PM
> It seems like there should be something special about that
> location - a
> tetrahedral center flanked by two rigid groups, but I
> don't know just
> how important that necessarily is. Have you tried just
> assigning the
> normal parameters for an alkane CH2 group (opls_136) to
> your atom in
> question?
>
> Just an idea, but I have no idea if this is a unique
> situation that
> requires unique parameter development.
>
> -Justin
>
> hhhh huan wrote:
> > 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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >> _______________________________________________
> >>
> >>>>> gmx-users mailing list
> >>>>>
> >> gmx-users at gromacs.org
> >>
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> >>
> >>>>> Please search the archive at
> >>>>>
> >>>>>
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> posting!
> >>>>
> >>>>
> >>>>> Please don't post (un)subscribe
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> >>>>>
> >> 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
> >>
> >>>> ========================================
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> ========================================
> >>
> >> 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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> >>
> >
> >
> >
> >
> >
>
> --
> ========================================
>
> 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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