[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 18

[Mijiddorj Batsaikhan]

I think that Husen, you shoud add your gromacs installed director
/usr/local/gromacs/bin: to $PATH in /etc/bashrc.
On Apr 5, 2016 6:00 PM, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:

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> Today's Topics:
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>    1. Gromacs 5.1.2 installation problem (Husen R)
>    2. Re: Gromacs 5.1.2 installation problem (James Graham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Apr 2016 14:19:15 +0700
> From: Husen R <hus3nr at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Gromacs 5.1.2 installation problem
> Message-ID:
>         <CACPfdUuJO4wjbYuLPcSoVyqvDtgg_UmH=
> LLeSzPLcBSPqcgzhg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 5 Apr 2016 10:11:03 +0100
> From: James Graham <J.A.Graham at soton.ac.uk>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Gromacs 5.1.2 installation problem
> Message-ID: <57038127.9090009 at soton.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> 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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> End of gromacs.org_gmx-users Digest, Vol 144, Issue 18
> ******************************************************
>