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.

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Presentation transcript:

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

Itacuruça (Brazil), E2GRIS1, – Summary 2 Introduction Computational Details Simulation Example Perspectives

Itacuruça (Brazil), E2GRIS1, – Introduction 3 Molecular Dynamics GROMACS

Itacuruça (Brazil), E2GRIS1, – Molecular Dynamics 4

Itacuruça (Brazil), E2GRIS1, – Molecular Dynamics 5 Simulations are classical Atoms are subjected to Newton’s Laws of Motion:

Itacuruça (Brazil), E2GRIS1, – Force Fields 6 Parameterized with experimental or ab initio data Expressions include several terms, describing relevant physical interactions

Itacuruça (Brazil), E2GRIS1, – Force Fields: Bonds 7

Itacuruça (Brazil), E2GRIS1, – Force Fields: Angles 8

Itacuruça (Brazil), E2GRIS1, – Force Fields: Dihedrals 9

Itacuruça (Brazil), E2GRIS1, – Force Fields: Dihedrals 10

Itacuruça (Brazil), E2GRIS1, – Update Positions 11 Leap-Frog Algorithm:

Itacuruça (Brazil), E2GRIS1, – Results 12 ATOMIC TRAJECTORIES: Thermodynamic Properties Relevant vibrations Receptor/Ligand complex formation Cannot be used to study reaction

Itacuruça (Brazil), E2GRIS1, – 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)

Itacuruça (Brazil), E2GRIS1, – 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

Itacuruça (Brazil), E2GRIS1, – Execution of Simulation 15

Itacuruça (Brazil), E2GRIS1, – COMPUTATIONAL DETAILS

Itacuruça (Brazil), E2GRIS1, – Installation 17 Requisites: gcc and possibly gfortran or binutils FFTW (Fastest Fourier Transform in the West - ) MPI Library (such as LAM or MPICH) The configuration of the source and makefiles is completely automated using GNU autoconf

Itacuruça (Brazil), E2GRIS1, – 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

Itacuruça (Brazil), E2GRIS1, – 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

Itacuruça (Brazil), E2GRIS1, – 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

Itacuruça (Brazil), E2GRIS1, – 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.

Itacuruça (Brazil), E2GRIS1, – Force Evaluation 22  Bonded forces fixed lists  Nonbonded forces dynamic lists  calculate distances (r)  calculate 1/r

Itacuruça (Brazil), E2GRIS1, – Nonbonded Forces 23 Neighbour Searching ij cutoff (i,j) r < r

Itacuruça (Brazil), E2GRIS1, – SIMULATION EXAMPLE

Itacuruça (Brazil), E2GRIS1, – Molecular System 25 HIV-Protease solvated with water: atoms

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

Itacuruça (Brazil), E2GRIS1, – 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)

Itacuruça (Brazil), E2GRIS1, – Perspectives 28 Treatment of large systems, such as membrane proteins Longer simulation times (microseconds) These would take several years!!!!