Molecular Simulation at MCSR Brian W. Hopkins Mississippi Center for Supercomputing Research 9 October 2008.

Slides:

Advertisements

Similar presentations

Time averages and ensemble averages

Advertisements

Ab Initio and Effective Fragment Potential Dynamics Heather M. Netzloff and Mark S. Gordon Iowa State University.

Mapping the Free Energy Landscape of HIV-1 TAR RNA with Metadynamics Tyler J. Mulligan 1, Harish Vashisth 2 1 M.S. Student, Department of Chemical Engineering,

Molecular Simulations of Metal-Organic Frameworks

1 NAMD - Scalable Molecular Dynamics Gengbin Zheng 9/1/01.

A Digital Laboratory “In the real world, this could eventually mean that most chemical experiments are conducted inside the silicon of chips instead of.

Abhinav Bhatele, Laxmikant V. Kale University of Illinois at Urbana-Champaign Sameer Kumar IBM T. J. Watson Research Center.

Abhinav Bhatele, Laxmikant V. Kale University of Illinois at Urbana-Champaign Sameer Kumar IBM T. J. Watson Research Center.

Chemistry in Parallel Computing Brian W. Hopkins Mississippi Center for Supercomputing Research 18 September 2008.

Molecular Dynamics Simulation (a brief introduction)

The Protein Folding Problem David van der Spoel Dept. of Cell & Mol. Biology Uppsala, Sweden

Temperature at the western boundary (T west ) required at each time-step Timestep 1: T west = 0 o C Timestep 2: T west = -1 o C Timestep 3: T west = -2.

StreamMD Molecular Dynamics Eric Darve. MD of water molecules Cutoff is used to truncate electrostatic potential Gridding technique: water molecules are.

Molecular Dynamics Molecular dynamics Some random notes on molecular dynamics simulations Seminar based on work by Bert de Groot and many anonymous Googelable.

MD SIMULATION OF TATA-BOX DNA: PME CALCULATIONS AND THE EFFECT OF ELECTROSTATIC CUT-OFF Jian Sun 1, Nina Pastor 2, Harel Weinstein 1 1 Dept. of Physiology.

1 CE 530 Molecular Simulation Lecture 2 David A. Kofke Department of Chemical Engineering SUNY Buffalo

Joo Chul Yoon with Prof. Scott T. Dunham Electrical Engineering University of Washington Molecular Dynamics Simulations.

Water cluster- silica collision Water cluster, 104 H 2 O Simulation time, 17ps NVE simulations O 1560 Si atoms Molecular mass g/mole.

An Introduction to Molecular Dynamics Simulations Macroscopic properties are often determined by molecule-level behavior. Quantitative and/or qualitative.

Bioinf. Data Analysis & Tools Molecular Simulations & Sampling Techniques117 Jan 2006 Bioinformatics Data Analysis & Tools Molecular simulations & sampling.

Statistical Mechanics of Proteins

Ana Damjanovic (JHU, NIH) JHU: Petar Maksimovic Bertrand Garcia-Moreno NIH: Tim Miller Bernard Brooks OSG: Torre Wenaus and team.

To create a flexible, extensible and reusable molecular modeling environment. Construction of a library for molecular modeling using a common data model.

Algorithms and Software for Large-Scale Simulation of Reactive Systems _______________________________ Ananth Grama Coordinated Systems Lab Purdue University.

Network for Computational Nanotechnology (NCN) Purdue, Norfolk State, Northwestern, MIT, Molecular Foundry, UC Berkeley, Univ. of Illinois, UTEP Polymer.

Javier Junquera Molecular dynamics in the microcanonical (NVE) ensemble: the Verlet algorithm.

Ps ns ss ms nm mm mm Ab-initio methods Statistical and continuum methods Atomistic methods.

Simulating PEO melts using connectivity-altering Monte Carlo Simulating PEO melts using connectivity-altering Monte Carlo by Collin D. Wick and Doros N.

Beckman Institute, UIUCNIH Resource for Biomolecular Modeling and Bioinformatics Molecular Dynamics Method 1 James Phillips Theoretical.

Molecular Dynamics Collection of [charged] atoms, with bonds – Newtonian mechanics – Relatively small #of atoms (100K – 10M) At each time-step – Calculate.

Molecular Dynamics A brief overview. 2 Notes - Websites "A Molecular Dynamics Primer", F. Ercolessi

Scheduling Many-Body Short Range MD Simulations on a Cluster of Workstations and Custom VLSI Hardware Sumanth J.V, David R. Swanson and Hong Jiang University.

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

Molecular Dynamics Simulation

ALGORITHM IMPROVEMENTS AND HPC 1. Basic MD algorithm 1. Initialize atoms’ status and the LJ potential table; set parameters controlling the simulation;

Inelastic Deformation in Shock Loaded PETN Reilly Eason and Thomas D. Sewell Department of Chemistry University of Missouri-Columbia Funded by Defense.

Molecular Dynamics simulations

Molecular simulation methods Ab-initio methods (Few approximations but slow) DFT CPMD Electron and nuclei treated explicitly. Classical atomistic methods.

Covalent interactions non-covalent interactions + = structural stability of (bio)polymers in the operative molecular environment 1 Energy, entropy and.

Molecular Simulation of Reactive Systems. _______________________________ Sagar Pandit, Hasan Aktulga, Ananth Grama Coordinated Systems Lab Purdue University.

Algorithms and Software for Large-Scale Simulation of Reactive Systems _______________________________ Metin Aktulga, Sagar Pandit, Alejandro Strachan,

Comparative Study of NAMD and GROMACS

Molecular Mechanics (Molecular Force Fields). Each atom moves by Newton’s 2 nd Law: F = ma E = … x Y Principles of M olecular Dynamics (MD): F =

1 Molecular Simulations Macroscopic EOS (vdW, PR) Little molecular detail Empirical parameters (  ) Seeking understanding of complex systems Surfactants.

Dynameomics: Protein Mechanics, Folding and Unfolding through Large Scale All-Atom Molecular Dynamics Simulations INCITE 6 David A. C. Beck Valerie Daggett.

Graphical Display of a Physics Simulation Steven Oetjen TJHSST Computer Systems Lab

Chapter 4 Forming Compounds. Chemical Bonding Chemical bond-the attractive force that holds ions together.  Chemical bonds form because atoms are losing.

Molecular dynamics (MD) simulations  A deterministic method based on the solution of Newton’s equation of motion F i = m i a i for the ith particle; the.

Symmetry in crystals. Infinitely repeating lattices.

Parallel Molecular Dynamics A case study : Programming for performance Laxmikant Kale

Molecular Simulation at MCSR Brian W. Hopkins Mississippi Center for Supercomputing Research 9 October 2008.

Flexibility and Interoperability in a Parallel MD code Robert Brunner, Laxmikant Kale, Jim Phillips University of Illinois at Urbana-Champaign.

Simulation Study of Phase Transition of Diblock Copolymers

Bonding and Structure in Solids

Simulation of Self-Assembly of Ampiphiles Using Molecular Dynamics

Molecular dynamics (MD) simulations

DL_POLY Miguel A. Gonzalez Institut Laue-Langevin

Molecular Modelling - Lecture 3

Physics-based simulation for visual computing applications

Molecular dynamics (MD) simulations

TEST RECOVERY One Key Recovery Disk Recovery.

Large Time Scale Molecular Paths Using Least Action.

Liouville formulation (4.3.3)

Molecular simulation methods

Molecular Geometry.

Experimental Overview

? Flow chart of a molecular dynamics simulation

Basic procedure for MD simulations

Atomic Detail Peptide-Membrane Interactions: Molecular Dynamics Simulation of Gramicidin S in a DMPC Bilayer Dan Mihailescu, Jeremy C. Smith Biophysical.

Presentation transcript:

Molecular Simulation at MCSR Brian W. Hopkins Mississippi Center for Supercomputing Research 9 October 2008

What We’re Doing Here Talk about molecular simulation procedures. Talk about available simulation programs. Discuss user simulation needs and program options.

Simulation: Anatomy of A Program Read in sim paramters, atomic coordinates and topology. Begin Timestepping –Apply periodic boundary conditions. –Build neighbor list. –Compute bonded forces. –Compute short-rang nonbonded forces. –Compute electrostatic forces. –Integrate forward in time. Write atomic positions, velocities and forces. Take data for statistical accumulators. –Repeat. End timestepping. Print restart data.

Program Anatomy: Read Control nafion #restart temperature steps timestep ps ensemble nve evbconv 1e-6 movlp 1 cutoff 10.0 angstrom rvdw 9.0 angstrom delr 0.00 angstrom

Program Anatomy: Read Config hcl in water …… OW E E E E E E E E E+03 HW E E E E E E E E E+03 HW E E E E E E E E E+02 …

Program Anatomy: Read Topology UNITS kcal MOLECULAR TYPES 4 FLEXIBLE-TIP3P-Water NUMMOLS 332 atoms 3 OW HW BONDS 2 harm harm ANGLES 1 harm FINISH …… vdw 9 OW OW lj OT OW lj HT OW lj

Program Anatomy: Set up Cell