Symulacje dynamiki molekularnej dla układów biologicznych

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  • Temat: Symulacje dynamiki molekularnej dla układów biologicznych
  • Data: 25 kwietnia (piątek), godz. 9.15
  • Miejsce: Wrocław, sala WCSS, bud. D-2 PWr, p. 101/7 (Mapa)
  • Prowadząca: dr Katarzyna Maksimiak z Michigan State University
  • Materiały: program (pdf)

Program

LECTURE

Title: Symulacje dynamiki molekularnej dla układów biologicznych.

Abstract: Molecular dynamics simulations is one of the most useful tools to simulate the dynamic behavior of biological macromolecules and, thereby, to understand the physical basis of their structure and function. The simulation can provide detailed information of the fluctuations and conformational changes of biopolymers, e.g. proteins and nucleic acids. With continuing advances in the methodology and the speed of computers, molecular dynamics are being extended to larger systems and longer time scales. This can give possibilities to study the behavior of the system, which cannot be investigated experimentally.

The goal of this lecture is to provide an overview of the theoretical basis of classical molecular dynamics simulations with common scenario of simulations using NAMD1 program, which is recently one of the most popular tools to run molecular dynamics.

References
  1. http://www.ks.uiuc.edu/Research/namd/


TUTORIAL

Title: Molecular dynamics of enzyme-DNA complexes

Goals: To learn how to run molecular dynamics (MD) using the program NAMD1.

  1. Learning how to prepare molecule for MD simulation.
  2. Learning about common steps in MD simulation.
  3. Analyzing the results after each step, in particularly after heating and equilibrium.
  4. Making movie from trajectory data.

Structure: 1DNK1

Programs: NAMD2.62, VMD1.8.6.3

Platforms: Linux System

Force Field: CHARMM5

References
  1. Weston, S.A., Lahm, A., Suck, D. , J.Mol.Biol. 226:1237-1256, 1992
  2. http://www.ks.uiuc.edu/Research/namd/
  3. http://www.ks.uiuc.edu/Research/vmd
  4. MacKerell AD, Jr., Bashford D, Bellott M, Dunbrack JD, Evanseck MJ, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewcz-Kuczera J, Yin D, Karplus M. J. Phys. Chem. B 1998; 102: 3586-3616.