[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

Vitaly Chaban chaban at univer.kharkov.ua
Tue Sep 16 23:36:09 CEST 2008

>> I am a beginner for Gromacs. I am using the latest version  Gromacs 4.0
>> beta1. Then I follow the tutorial part: Introduction to MD 
>> <http://md.chem.rug.nl/education/mdcourse/> by the Groningen group. 
>> Compiling is ok, but I always get the Segmentation fault when I use 
>> command : genbox -cp minimized_box.gro -cs spc216.gro -o 
>> minimized_water.gro -p aki.top. Also I get the same problem when i try 
>> other exercises.  Does anyone has same problem like me ? or can anyone
>> give me a hint for that?  Thanks in advance. 
> It sounds like your installation is faulty.  What architecture are you running 
> on?  What compilers did you use?
> If you are just starting out, it is probably better to use an official release 
> of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development.
> -Justin

A few days ago I experienced the same problem with genbox in gmx-4.0-beta. I didn't
pay much attention to it since it's just CVS but it actually was
permanently present. gmx-4.0 compiled with the same parameters on the same system does not
give this error.

There's no such problem in gmx-3.3.3 and earlier ones. I would suggest
you to use them to avoid much headache.

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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