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

[Justin A. Lemkul]

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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>>>   
>>>       
>> -- 
>> ========================================
>>
>> 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

========================================