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GROMACS

GROMACS. E2GRIS1 André A. S. T. Ribeiro – UFRJ (Brazil) Itacuruça (Brazil), 2-15 November 2008. Summary. Introduction Computational Details Simulation Example Perspectives. Introduction. Molecular Dynamics GROMACS. Molecular Dynamics. Molecular Dynamics. Simulations are classical

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GROMACS

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  1. GROMACS E2GRIS1 André A. S. T. Ribeiro – UFRJ (Brazil) Itacuruça (Brazil), 2-15 November 2008

  2. Summary Introduction Computational Details Simulation Example Perspectives

  3. Introduction • Molecular Dynamics • GROMACS

  4. Molecular Dynamics

  5. Molecular Dynamics Simulations are classical Atoms are subjected to Newton’s Laws of Motion:

  6. Force Fields Parameterized with experimental or ab initio data Expressions include several terms, describing relevant physical interactions

  7. Force Fields: Bonds

  8. Force Fields: Angles

  9. Force Fields: Dihedrals

  10. Force Fields: Dihedrals

  11. Update Positions Leap-Frog Algorithm:

  12. Results ATOMIC TRAJECTORIES: Thermodynamic Properties Relevant vibrations Receptor/Ligand complex formation Cannot be used to study reaction

  13. GROMACS • GROningen MAchine for Chemical Simulations • GROMACS consists of more than fifty programs. These can be divided in three major classes: • Preparation of Input • Execution of Simulation (mdrun) • Analysis of Output • Programs are command-line based, written mostly in C. Current major developers: • Erik Lindahl (Sweden) • David van der Spoel (Sweden) • Berk Hess (Germany)

  14. GROMACS: Preparation of Input Read system’s information (nuclear coordinates, simulation time, temperature, etc) Determine list of interactions Divide system over processor nodes Produce binary file containing relevant data for mdrun

  15. Execution of Simulation

  16. COMPUTATIONAL DETAILS

  17. Installation Requisites: gcc and possibly gfortran or binutils FFTW (Fastest Fourier Transform in the West - http://www.fftw.org ) MPI Library (such as LAM or MPICH) The configuration of the source and makefiles is completely automated using GNU autoconf

  18. Parallel MD “For better efficiency, portability and for historical reasons we chose a message-passing implementation. Our program was initially designed for a special-purpose machine with a ring architecture and without tools for data-parallel programming.” Berendsen H.J.C., van der Spoel D., van Drunen R. Comput. Phys. Commun. 91:43–56, 1995

  19. Parallel MD 2 • Force Evaluation -> O(N ) • During input preparation, grompp assigns to each processor a number of interactions and a number of particles (home particles) to be updated in each simulation step

  20. Parallel MD • Read Input Data (MASTER NODE) • Communicate Input Data through the ring • Execute MD Loops until specified number of steps (nsteps) • Print Output

  21. Parallel MD: MD Loop • Communicate all coordinates • Calculate the forces specified for the current node • Communicate forces through the ring • Sum forces for the home particles • Update positions and velocities for the home particles.

  22. Force Evaluation • Bonded forces fixed lists • Nonbonded forces dynamic lists • calculate distances (r) • calculate 1/r

  23. Nonbonded Forces (i,j) r < r ij cutoff Neighbour Searching

  24. SIMULATION EXAMPLE

  25. Molecular System HIV-Protease solvated with water: 86992 atoms

  26. Simulation Parameters • Temperature: 300 K • Pressure : 1 bar • dt : 0.002 ps • nsteps : 5,000,000 (10 ns) • cubic box • Force Field : OPLS-AA

  27. Simulation Details • Input file (binary) : 119 MB • distribute_parts sends 90 MB of data through the ring • Each MD iteration sends approximately 3 MB through the ring (coordinates and forces)

  28. Perspectives • Treatment of large systems, such as membrane proteins • Longer simulation times (microseconds) These would take several years!!!!

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