[gmx-users] pdb2gmx illegal instruction (core dumped)

[Md. Imrul Reza Shishir]

Thank you David van der Spoel. I compile gromacs in my own laptop and I run
on the same machine. Your guideline working properly. I reinstall gromacs
and now all okk..

regards and thank you.

Md Imrul Reza Shishir
On Jan 28, 2016 4:47 PM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:

> On 28/01/16 08:33, Md. Imrul Reza Shishir wrote:
>
>> Hi Everyone.
>> I use Lenovo A6-7310 (4 core 2MB cache memory) processor in my laptop. I
>> install Gromacs 5.0.7 with latest cmake-3.4.2 and fftw-3.3.4. I use below
>> Cmake command to install.
>>
>> "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON"
>>
>> I am newbies gromacs user. I am trying to execute the Bevan Lab tutorial
>> (Lysozyme in water). my first command is
>>
>> "gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce"
>>
>> It execute properly. But when i execute number 15 force
>> field(OPLS-AA/L) at the end there is a massage "illegal instruction
>> (core dumped)". And in my directory only topology file create. No
>> gromacs output file Created "1AKI_processed.gro".
>>
>> Illegal instruction means the program was compiled for another machine
> than what it is run on. Did you really compile the program on the same
> machine you are running on?
>
> In that case you may need to manually set the GMX_SIMD flag when running
> cmake, e.g.
> -DGMX_SIMD=SSE4.1
>
>
> Any help greatly appreciated.
>>
>> ​Bst Regards​
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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