1. Directory organization

The workflow for setting up, running, and analysing a simulation consists of multiple and rather different steps. It is useful to perform these different steps in separate directories in order to avoid overwriting files or using wrong files.

For this tutorial the suggested directory layout is the following:

coord/
top/
solvation/
emin/
posres/
MD/
analysis/

You will work through these directories in sequence.

Short description of the directories

coord

original PDB files

top

topology files (.top, .itp)

solvation

add solvent and ions

emin

energy minimization

posres

short MD simulation with position restraints on the heavy protein atoms, to allow the solvent to equilibrate around the protein without disturbing the protein structure

MD

MD simulation (typically, you will transfer the md.tpr file to a supercomputer, run the simulation there, then copy the the output back to this trajctory)

analysis

analyze the simulations in (sub)directories under analysis, e.g.

analysis/RMSD
analysis/RMSF
...

The subdirectories depend on the specific analysis tasks that you want to carry out. The above directory layout is only a suggestion but in practice some sort of ordered directory hierarchy has proven very useful.

The command snippets below assume the above directory layout. We will not explicitly list all the necessary cd commands to change directories. The workflow is such that each step is carried out inside the appropriate directory and relative paths are used to access files from previous steps. It should be clear from the context in which directory the commands are to be executed. If you get a File input/output error from grompp (or any of the other commands) then check that you are able to see the file by just doing a ls ../path/to/file from where you are in the file system. If you can’t see the file then check (1) that you are in the correct directory, (2) that you have created the file in a previous step.