GROMACs GROningen MAchine for Chemical Simulations Eliana Bohorquez Puentes Nicolas Ortiz Gonzalez

Overview GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non- bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Tools GROMACs contains several tools and commands that allow a diverse range of biological functions to be performed. The tools we most used were: Mdrun Mpimdrun

mdrun Mdrun is the main command of the AutoDock portfolio. It begins the basic molecular dynamics calculus after all the other parameters have been set.

mpimdrun This command executes the same commands found in mdrun, but it’s the process of execution which is different. This command executes molecular dynamic functions as an MPI application, thus distributing the number of steps between several computers.

mpimdrun The distribution of functions and use of checkpoints reduces the time needed to finish a single simulation, and allows for several simulations to run in parallel.

Resources needed A single GROMACs simulation can take between hours, depending on the initial conditions, and several running at the same time can take more. Resources taken on the computer are defined, but more cores mean faster simulations, which is why more infrastructure is much desired.

Use on the GISELA Infrastructure We consider that incorporating GROMACs into the GISELA infrastructure will allow several biologists and chemical engineers to run molecular dynamics simulations, thus helping them hone their results before conducting lab tests, and reducing costs, without the need of having the computational resources on campus.

Our own experience We here at the Universidad de Los Andes have worked with the chemical engineering department to run several molecular dynamics simulations. Many simulations are run in a single month on the Unacloud infrastructure.

Questions?