Workflow and Analysis Approaches for Molecular Dynamics Simulations Catania, September 21 st, 2010 Jens Krüger *, Georg Birkenheuer, Sebastian Breuers, Sandra Gesing, Martin Wewior, André Brinkmann, Dirk Blunk, Oliver Kohlbacher, Lars Packschies and Gregor Fels * Universität Paderborn, Universität zu Köln, Eberhard-Karls-Universität Tübingen

Motivation Molecular simulations, in particular molecular dynamics simulations, are an increasingly powerful tool Many scientists have only a limited background in modern information technology Many scientists specialize on a particular application, neglecting competing options

Goals Representation of complex scientific simulation protocols as workflows, making them executable on grid resources Increasing availability and ease of use of grid resources Liferay/P-Grade based frontend Unicore as middleware Workflow submission via Unicore- Commandline-Client (UCC)

Concept Unicore UAS Cluster Portal Liveray Unicore RichClient Workflow Instanz UCC Unicore Workflow UAS SERVORC UAS

Equilibration of Proteins Proteins form databases (e.g. pdb.org) do not necessarily represent a native like conformation/configuration For all kind of production runs a minimization and an equilibration is an indispensable prerequisite Eases the work of experienced users Lowers the hurdle for newbie's

UseCase: Gromacs_EQ structure (pdb/gro) topology (top/itp) EM.mdp (mdp) pdb2gmx structure (pdb) editconf box (pdb) genbox Solvated (pdb) grompp adj. Top. (top/itp) topol.tprmdout.mdp

mdrun ener.edr traj.trrtraj.xtc md.log state.cpt SYSTEM_EM. pdb grompp mdrun topol.tprmdout.mdp ener.edrtraj.trrtraj.xtc md.logstate.cpt SYSTEM_EQ. pdb FULL.mdp (mdp) g_energyxmgrace Analysis.jpg g_energyxmgrace Analysis.jpg

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Ongoing Work Bigger – More UseCases to cover a broader range of scientific problems – More analysis options including interactive visualization of relevant results Better – Exit code capturing and intelligent error code parsing with smart interpretations displayed within the portlet Faster – Automatic job distribution on multiple clusters using the Unicore Service Orchestrator and/or WS-PGRADE

Collaborators BMBF (Förderkennzeichen 01IG09006) Paderborn, Organic Chemistry Gregor Fels Jens Krüger Brigitta Elsässer Markus Tusch Iris Baum Paderborn, PC 2 André Brinkmann Georg Birkenheuer Oliver Niehörster Matthias Keller Jens Simon Andreas Krawinkel Holger Nietsche Axel Keller Berlin, Zuse Institut Thomas Steinke Patrick Schäfer Nico Kruber Tübingen, Bioinformatic Oliver Kohlbacher Sandra Gesing Köln, Organic Chemistry Dirk Blunk Sebastian Breuers Köln, RRZ Lars Packschies Martin Wewior Klaus Warzecha Dresden, ZIH Ralf Müller- Pfefferkorn Richard Grunzke... and many associated partners.