Molecular Dynamics Essentials

The pages linked here will hopefully be useful for anyone getting started with MD, or as a review for more experienced molecular dynamicists. I will add pages as I see fit, but I encourage anyone to add/edit as they encounter problems and solutions that could be of general use. These articles, as of now, will mostly be tailored to GROMACS, PLUMED, and VMD, although those are subject to change as the group evolves.

Since the following pages will assume a basic level of familiarity with the above softwares, I highly recommend going through some online tutorials for some of the basics. Below are the ones I have historically found to be the most helpful - I recommend moving in the order of VMD - GROMACS - PLUMED, as they tend to build on one another.

• VMD: A fairly extensive tutorial from UIUC can be found here. For beginners, the 'Working with a Single Molecule' and 'Trajectories and Movie-Making' sections will be a sufficient introduction. Focus on getting the basics down, and you can return to image rendering/movie making once you have a good handle on MD in general. A more advanced treatment of structure rendering can be found at VMD Rendering Guide. More advanced users might find the other sections of the UIUC tutorial, particularly the tcl scripting section, useful. On Midway, one can load vmd by running module load vmd. Note that the VMD graphic interface will only work on login nodes or interactive sessions on weare-dinner2. 

• GROMACS: Lysozyme in Water tutorial out of Virginia Tech. This assumes GROMACS 2018 or later - luckily, we have GROMACS 2019.4 installed on Midway (see the software section of Running Jobs on Midway and GROMACS 2019.4 with GPU Support). After this, you should be familiar with elements of an .mdp and .top files, concepts of system building and equilibration, and basic analysis techniques. I also highly recommend reading through relevant sections of the GROMACS User Guide and Reference Manual (the user guide, in particular, will be very helpful for beginners). On Midway, one can load GRACE (for measuring and visualizing volume, temperature, pressure, etc.) by running module load grace. After this, one can use GRACE by using the xmgrace command. For GROMACS GPU support on Midway, see GROMACS 2019.4 with GPU Support. Feel free to visualize your trajectories using VMD. As a note, using the installation on midway, you will need to use the gmx\_mpi command instead of simply gmx. If you want to run a simulation on more than one core, you will need to run the job by invoking mpirun. For example, to run a simulation on 4 cores, one needs to run mpirun -np 4 gmx\_mpi ... .

• PLUMED: There are tons of online tutorials available, of varying levels of complexity. I like the Trieste tutorial for basics of using PLUMED to analyze existing MD trajectories, and the Munster tutorial for using PLUMED and GROMACS to bias MD simulations, and reconstructing a potential of mean force by using umbrella sampling. Others are also useful, so feel free to browse. On Midway, PLUMED can either be loaded by itself (module load plumed) or as a package with GROMACS (source /project2/dinner/gromacs/sourceme.sh ) - see Running Jobs on Midway and GROMACS 2019.4 with GPU Support for more details). 

All of these tutorials should prove useful to you. I have historically found, though, that the most effective learning is done when trying to actually run the system you're interested in. So, while I highly recommend doing these tutorials, try not to spend forever to perfect every single one. At some point, it is more useful to move onto building and running your own system, and then returning to the tutorials with new eyes. To that end, I also recommend building your own system (Building a System With CHARMM-GUI), choosing your own parameters (MDP options), equilibrating that system (Energy Minimization and Equilibration), running some vanilla, equilibrium simulations, and then start some manipulation (often times driving the system, see PLUMED Tips and Tricks) and analysis (PLUMED Tips and Tricks and VMD as an Analysis Tool). Throughout, you should be visualizing your trajectories/structures (VMD Rendering Guide). 

Throughout any of these guides, if you find yourself with questions that you cannot find answers to by asking older grad students, or searching the internet, both GROMACS and PLUMED have very active user forums. You should feel free to post in the PLUMED google group or the GROMACS forum. Both are great resources for questions you cannot find the answers to otherwise. Just be sure to read the rules before posting (and read to see if your question has been asked before), and be very descriptive in your question.