[gmx-users] segmentation fault during MD

[Justin A. Lemkul]

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

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