[gmx-users] gromacs synaptic package manager
Justin A. Lemkul
jalemkul at vt.edu
Sat Oct 2 01:08:00 CEST 2010
ahmet yıldırım wrote:
> Dear Roland,
>
> Eventually I installed the installation steps with
> "./configure --prefix=$HOME/usr "as you said. can you send me the input
> file for test?
> I want to run a simulation. how can I do this?
>
Please do some tutorial material. I sent you the link before.
-Justin
> Thanks for your helps
>
>
> 2010/10/2 Roland Schulz <roland at utk.edu <mailto:roland at utk.edu>>
>
> Hi,
>
> either install as root by running:
> sudo make install
>
> or rerun the installation steps with
> ./configure --prefix=$HOME/usr
> to install it in your home directory.
>
> Roland
>
> 2010/10/1 ahmet yıldırım <ahmedo047 at gmail.com
> <mailto:ahmedo047 at gmail.com>>
>
> Dear justin,
>
> Thanks for your reply. I did that you said. I tried to install
> Gromacs 4.5.1but I failed it. I enter this line "
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make install " in
> terminal. What can I do? I am sorry. I am a new user.
>
> Thanks in advance
>
> 1. I installed fftw 3.2.2
> ab at ab-desktop:~/Masaüstü/ cd fftw-3.2.2
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure
> --enable-threads --enable-float
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make
> ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make install
>
> 2. I tried to install Gromacs 4.5.1
> ab at ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make
> ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make install
> Making install in include
> make[1]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> Making install in .
> make[2]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[3]: Entering directory
> `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[3]: Nothing to be done for `install-exec-am'.
> test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p
> "/usr/local/gromacs/include/gromacs"
> /bin/mkdir: cannot create directory `/usr/local/gromacs':
> Permission denied
> make[3]: *** [install-pkgincludeHEADERS] Error 1
> make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'
> make: *** [install-recursive] Error 1
>
>
>
> 2010/10/1 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>
>
>
>
> ahmet yıldırım wrote:
>
> Hi,
>
> I've installed GROMACS 4.0.3 and MPI libraries using
> Ubuntu 9.04 Synaptic Package Manager. What else should I do?
> I want to run a simulation in parallel on a single PC.
> Which commands should I enter the terminal?
>
>
> If I were you, I would uninstall this version (which is
> outdated by nearly 2 years!) and get version 4.5.1.
> Installing from source is quite easy. Not only will you
> benefit from hundreds of bug fixes and enhancements, but
> running in parallel on a multi-core machine is no longer
> MPI-dependent, making it somewhat easier.
>
> For usage and instructions, see the manual and any of the
> numerous tutorials linked here:
>
> http://www.gromacs.org/Documentation/Tutorials#General
>
> -Justin
>
>
> Thanks a lot for any instruction.
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Ahmet YILDIRIM
>
> --
>
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> --
> Ahmet YILDIRIM
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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