Linux Tutorial
This is an update on a manual I initially wrote in Spanish, way back
in the day at the G.Q.T. (Grupo de Quimica Teorica)
- Linux Tutorial English
- Linux Tutorial Spanish
The following are some useful commands:
free -m ///Shows how much RAM your computer has.
uname -a ///Tells you what distro and kernel version u have.
wget -r -l1 --no-parent -nd http://www.eden.rutgers.edu/~esguerra/scripts /// Will get all files in the directory
Linux Installation & Packages.
I learned linux using Slackware and RedHat. Then switched to Fedora
Linux and now (2009) I'm using Ubuntu/Debian.
At the beggining of 2006 I changed from my beloved Slackware to Fedora
since it seemed easier to upgrade kernels with it and also because yum
can be used for easier package installation. Now (2009) its easier to solve
dependencies automatically using apt-get from Ubuntu.
The following is a list of programs which I need everytime I do a new
Linux install, or when I upgrade versions. This might at some point
point towards creating a customized Linux version for computational
chemists and bioinformaticians.
List of programs needed in personal installation:
python (numpy and matplotlib)
django
mysql
pymol
molden
vmd
openrasmol
sirius
molekel
gopenmol
chimera
king
prekin
molscript
raster3d
3DNA
apbs
amber
gamess
octave
R
gnuplot
ifort
acroread
LaTeX
Xfig
OpenOffice
JabREF
Scripts in ~/bin:
pdb_get \\python script to get pdb files directly to terminal.
plot \\perl script for using gnuplot from the terminal.
PPdistance \\script to find distance matrix.
helivec \\script to extract helical axis vectors from 3DNA output.
xtractNkin \\script to make a king plot of helical axis vectors, depends on prekin.
get_bsparam \\get base-step parameters from file.out and organize them for R input.
Customization files in user root:
.emacs
.bashrc
.bash_profile