Integrate the GROMACS Bash scripts

[mkjensen]

Integrate the Bash scripts used for communicating with GROMACS. Ideally, no Bash scripts should exist, and the user should provide a PDB file, a TOP file, and MDP files for energy evaluation and energy optimization.

[gmongell]

Hi Martin, after a bit of googling GROMACS and bash scripting, I came across your git page. I'm wondering how much time you've spent on bash scripting with GROMACS. I've worked on things like submitting and analyzing lots of jobs -- performing trjconv and g_density etc on many files in different job folders -- however the next step is to plot these. Have you written any gnu plot codes for GROMACS?

[mkjensen]

The scripts I wrote are already included in the repository. As far as I remember, I did not use Gnuplot but there may be a few plots created using R. I can recommend the GROMACS mailing lists which helped me getting started.