1. www.eu-eela.org E-science grid facility for Europe and Latin America E2GRIS1 André A. S. T. Ribeiro – UFRJ (Brazil) Itacuruça (Brazil), 2-15 November 2008 GROMACS

2. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Summary 2 Introduction Computational Details Simulation Example Perspectives

3. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Introduction 3 Molecular Dynamics GROMACS

4. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Molecular Dynamics 4

5. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Molecular Dynamics 5 Simulations are classical Atoms are subjected to Newton’s Laws of Motion:

6. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Fields 6 Parameterized with experimental or ab initio data Expressions include several terms, describing relevant physical interactions

7. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Fields: Bonds 7

8. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Fields: Angles 8

9. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Fields: Dihedrals 9

10. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Fields: Dihedrals 10

11. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Update Positions 11 Leap-Frog Algorithm:

12. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Results 12 ATOMIC TRAJECTORIES: Thermodynamic Properties Relevant vibrations Receptor/Ligand complex formation Cannot be used to study reaction

13. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 GROMACS 13 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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 GROMACS: Preparation of Input 14 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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Execution of Simulation 15

16. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 16 COMPUTATIONAL DETAILS

17. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Installation 17 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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Parallel MD 18 “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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Parallel MD 19 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 2

20. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Parallel MD 20  Read Input Data (MASTER NODE)  Communicate Input Data through the ring  Execute MD Loops until specified number of steps (nsteps)  Print Output

21. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Parallel MD: MD Loop 21  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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Force Evaluation 22  Bonded forces fixed lists  Nonbonded forces dynamic lists  calculate distances (r)  calculate 1/r

23. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Nonbonded Forces 23 Neighbour Searching ij cutoff (i,j) r < r

24. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 24 SIMULATION EXAMPLE

25. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Molecular System 25 HIV-Protease solvated with water: 86992 atoms

26. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Simulation Parameters 26 Temperature: 300 K Pressure : 1 bar dt : 0.002 ps nsteps : 5,000,000 (10 ns) cubic box Force Field : OPLS-AA

27. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Simulation Details 27 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. www.eu-eela.eu Itacuruça (Brazil), E2GRIS1, 2.11.2008 – 15.11.2008 Perspectives 28 Treatment of large systems, such as membrane proteins Longer simulation times (microseconds) These would take several years!!!!