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

Fri, 04 Jul 2008 07:15:09 -0700 


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 <[EMAIL PROTECTED]> wrote:


  

From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] segmentation fault during MD
To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 
<[email protected]>
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

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

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