ahmedo047
October 5th, 2010, 02:07 PM
I want to install gromacs-4.5.1 on ubuntu 9.04.
1. I installed fftw-3.2.2 as following
ab@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
ab@ab-desktop:~/Masaüstü/fftw-3.2.2
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 sudo make
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 sudo make install
In this way, FFTW-3.2.2 installed /usr/local/include and /usr/local/bin directories--(I have root permissions to write there)
2. I installed gromacs-4.5.1 as following
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install
In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have root permissions to write there)
I try running the following command,
$luck
there is error.
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 pdb2gmx -h
I've written the Gromacs Mail list before, but I get the answers as following:
1.In a normal Unix/Linux/Cygwin/MacOS environment you will need to know the location where GROMACS is installed, e.g. /usr/local/gromacs. In your shell configuration file (e.g. .bashrc for bash, or .cshrc / .tcshrc for tcsh) you should use a command analogous to:
source /usr/local/gromacs/bin/GMXRC near the end of that file.
(http://www.gromacs.org/Downloads/Installation_Instructions)
2."You need to either add the location of your Gromacs installation to your PATH (in whatever shell configuration file, likely .bashrc) or source GMXRC every time you log in to a new terminal. Once your Gromacs installation is recognized by your shell environment you can run all the commands."
3.You a suitably configured environment.
4.This is a fairly basic UNIX issue, and has nothing specific to do with GROMACS. You need to have an appreciation of what the UNIX environment is, and how you can "source" a file to adjust that environment. Once you understand the need to adjust the environment, you can see how "sourcing" GMXRC will solve some of your problems.
What should I do? how can I adjust the Environment?
Thanks in advance
1. I installed fftw-3.2.2 as following
ab@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
ab@ab-desktop:~/Masaüstü/fftw-3.2.2
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 sudo make
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 sudo make install
In this way, FFTW-3.2.2 installed /usr/local/include and /usr/local/bin directories--(I have root permissions to write there)
2. I installed gromacs-4.5.1 as following
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install
In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have root permissions to write there)
I try running the following command,
$luck
there is error.
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 pdb2gmx -h
I've written the Gromacs Mail list before, but I get the answers as following:
1.In a normal Unix/Linux/Cygwin/MacOS environment you will need to know the location where GROMACS is installed, e.g. /usr/local/gromacs. In your shell configuration file (e.g. .bashrc for bash, or .cshrc / .tcshrc for tcsh) you should use a command analogous to:
source /usr/local/gromacs/bin/GMXRC near the end of that file.
(http://www.gromacs.org/Downloads/Installation_Instructions)
2."You need to either add the location of your Gromacs installation to your PATH (in whatever shell configuration file, likely .bashrc) or source GMXRC every time you log in to a new terminal. Once your Gromacs installation is recognized by your shell environment you can run all the commands."
3.You a suitably configured environment.
4.This is a fairly basic UNIX issue, and has nothing specific to do with GROMACS. You need to have an appreciation of what the UNIX environment is, and how you can "source" a file to adjust that environment. Once you understand the need to adjust the environment, you can see how "sourcing" GMXRC will solve some of your problems.
What should I do? how can I adjust the Environment?
Thanks in advance