[gmx-users] Re: segmentation fault during MD and develop parameter
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 5 13:25:02 CEST 2008
hhhh huan wrote:
> 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
>
>
>
Well, you've already decided that you need to develop some new
parameters, so there's really nothing left to be said. Read the
paper(s) that deal with OPLS force field development, and follow what
was done with respect to the parameter(s) you need to develop.
Be warned, this is an advanced topic, and I doubt your "headache" will
go away any time soon :-)
-Justin
>
>
> --- 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
>>>>
>>>> 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
>>
>>>>
>>>>
>>>>>> ========================================
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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 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
>>
>> ========================================
>>
>
>
>
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list