BioExcel Webinar #87:The GROMACS tutorial suite: from basic to advanced applications

BioExcel Webinar #87 The GROMACS tutorial suite: from basic to advanced applications Presenter: Alessandra Villa - KTH Royal Institute of Technology - Stockholm Webinar team: Alessandra Villa, Otto Andersson and Richard Norman BioExcel - Center of Excellence for Computational Biomolecular Research This webinar is being recorded 2 Audience Q&A session Please use the Q&A function at the bottom of Zoom application to tell us that you have a question. If you want us to read the question for you (just write no microphone) 3 After Webinar After webinar: you still have questions, pls ask them in the forum https://gromacs.bioexcel.eu/ 5 tags gmx-tutorial + topic Today’s Presenter 6 Alessandra was educated in chemistry and after aPh.D. in quantum chemistry she started to work in the field of classical molecular dynamics. Her main research interest is to elucidate how biomolecular interactions govern cellular processes. One of her current activities focuses on users community, user-drivendevelopment and training for the GROMACS software package within the BioExcel CoE 7 8 The GROMACS tutorial suite: from basic to advanced topics Alessandra Villa KTH Royal Institute of Technology [email protected] Outline ▪GROMACS overview ▪GROMACS tutorials overview ▪Tutorial knowledge map ▪Ideas behind tutorial design ▪Tutorial usage 9 GROMACS: a software for Molecular Dynamics simulations Newton’s equation of motion acceleration = force /mass 𝑑2𝑟𝑖 𝑑𝑡2=𝐹𝑖 𝑚𝑖 force = -slope of the potential 𝐹𝑖= − 𝜕 𝜕𝑟𝑖𝑉(𝑟1, 𝑟2… … … 𝑟𝑁) 𝑖 = 1……..Nparticles input/output GROMACS files preprocessing tools, md engine, postprocessing tools basic pipeline from pdb file -> energy minimization -> data production 18 How to run GROMACS efficiently Protein membrane MD liquid-liquid Density-fit simulation Enhance sampling techniques mass repartition multiple time steps Factor Xa CHARMM and AMBER force field Introduction to MD How to RUN GROMACS efficiently Optimal HPC usage and software usage allows to solve a biological/biochemical problem with maximizing the science for computational time With advantage for the society, the scientific community and technological development Efficient usage of CPU and GPU resource Tune the performance Run on multiple nodes Awareness of the range of possible simulations and available hardware is huge doi:10.5281/zenodo.10683366 how to run GROMACS efficiently on the LUMI supercomputer 20 Solvation free energy using AWH Umbrella sampling AWH basic Potential of mean force with AWH AWH advance Enhance sampling techniques Accelerate Sampling Calculate free energy using alchemical transformation Solvation free energy Ethanol –OPLS force field Ethanol - ethanthiol pyrimid-pyrimid folding process of the protein chigolin DNA base-pair opening Ideas behind GROMACS tutorial suite 21 •all the tutorials have been designed for training events •update and test according to GROMACS release cycle •Jupyter Notebook format –easy to deploy locally •deployment online using myBinder •hosted on GitLab (everybody can contribute) •distribute under CC-BY-4.0 license •build on a common template –user-driven •using simple show case 22 Jupyter Notebook Online –via my binder 23 Online –via my binder 24 Now we navigate 25 https://tutorials.gromacs.org/ How to run locally (I) ▪Install conda or miniconda on your laptop ▪Download the tutorial repo from tutorial.gromacs.org tutorial_name.zip ▪unzip tutorial_name.zip ▪cd tutorial_name ▪look for environment.yml (conda environment file) 26 more environment.yml 27 Audience Q&A session Please use the Q&A function at the bottom of Zoom application to tell us that you have a question. If you want us to read the question for you (just write no microphone) After the webinar And do not forget to fill the survey! 34 35 Next Webinar Webinar Series