The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations.
The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 40 participants. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions.
The tutorial shows you how to use NAMD and VMD for biomolecular modeling. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters.
The program VMD isdesigned for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein DataBank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule and can be used to animate and analyze the trajectory of a molecular dynamics simulation.More details, references and training material for both, NAMD and VMD, can be found at http://www.ks.uiuc.edu/