[gmx-users] Gromacs 5.1.2 installation problem

[Husen R]

Hello James,

Thank you for your reply and valuable information.

I tried running "gmx [command]" and it works.
Sorry for this fundamental question.

Regards,

Husen

On Tue, Apr 5, 2016 at 4:11 PM, James Graham <J.A.Graham at soton.ac.uk> wrote:

> Hi Husen,
>
> In GROMACS version 5.1 the default program naming scheme was changed so
> that everything is now part of the executable 'gmx'.  Because of this you
> need to use 'gmx pdb2gmx' (and e.g. 'gmx grompp', 'gmx mdrun') instead.
>
> The change was actually made in version 5.0, but they left an option to
> use it the old way as well.
>
> Regards,
> James
>
>
> On 05/04/16 08:19, Husen R wrote:
>
>> Dear all,
>>
>> I already installed gromacs-5.1.2 succesfully with the following
>> instruction :
>>
>> tar xfz gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2
>> mkdir build
>> cd build
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
>> make
>> make check
>> sudo make install
>> source /usr/local/gromacs/bin/GMXRC
>>
>> However, after finishing installation I can not use mdrun, pdb2gmx
>> (and possibly other commands).
>> The following is the error message when I tried to run pdb2gmx command.
>>
>> The program 'pdb2gmx' is currently not installed. You can install it by
>> typing:
>> sudo apt-get install gromacs
>>
>> I tried to find those commands using "locate" command but they're
>> doesn't exist as if gromacs is not installed.
>> Note : The installation directory /usr/local/gromacs is exist.
>>
>> anyone please tell me what will be the cause of this problem ?
>>
>> Regards,
>>
>>
>> Husen
>>
>
> --
> James Graham - PhD Student
> Institute for Complex Systems Simulation (ICSS)
> Computational Systems Chemistry
> University of Southampton, UK
>
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