This a tentative list of softwares/packages we should have in your Linux based desktop. Depending on purpose you may or may not need to install some of these packages.
>> gnuplot (plotting tool)
>> xmgrace (plotting tool)
>> ghostview (short form "gv", to view .ps file)
>> gimp (to edit images)
>> ps2pdf (to convert .ps file to .pdf file)
>> a2ps (to convert normal txt file to .ps file)
>> xpdf and xdvi
>> acroread (adobe reader: to view pdf files)
>> Latex (to write articles/books/thesis)
>> vmd (visualization software)
>> OCTAVE, MOLDEN
>> Packmol (Generate random initial configuration)
>> gcc compiler
>> java (some of the packages require java runtime distribution)
>> Intel fortran compiler (ifort: you may or may not intsall)
>> vlc (if you wish to see any media files)
>> lbfgs (for optimization algorithm)
>> Molecular Simulation Packages (DLPOLY, LAMMPS, GROMACS, TOOWHEE)
>> MATLAB (fitting tool, making 2D plot)
>> Dropbox (for file sharing)
>> Teamviewer ( for remote connection)
>> flash player
>> google chrome
>> cmake
>> perl
>> openmpi
>> fftw
>> Mendeley Desktop
>> vim (to edit files)
>> avogadro (to generate molecule pdb file)
>> gcc-c++
>> gcc-fortran