übung Protein Function Prediction.doc

übung: Molecular Dynamics Simulation of a Protein SS 2007 übung zu Struktur und Simulation (00.912) 17-Apr-07 1. Timeplan 1 2. Introduction 2 2.1. Calculations 2 3. Gromacs calculations 3 3.1. First MD run 4 3.2. Second MD run 5 4. Simple analysis 6 4.1. Energies 6 4.2. Fluctuations 6 5. Exchange of information 7 6. Assignment 7 7. Background and reference notes 9 7.1. Gromacs and the commands 9 7.2. The batch system 10 8. chimera / displaying structures / movies 11 Timeplan * Apr 17: set up simulations and put them in the batch system * 24 Apr: analysis of * energy * size * correlation function * 1 Mai: Ehren das Proletariat * 8 Mai: exchange of results between different people A brief report should be handed in by 15 Mai. Introduction It is assumed that * you remember how to get a file of coordinates from the protein databank (). * you can produce a simple x-y plot * you remember how to display a coordinate file, but see the notes on page?11. Calculations Different people will work on different proteins and at different temperatures. The simulations are rather realistic, but we will make a drastic simplification so as to save computer time. We will run on proteins in vacuo. There will be no solvent. This saves more than an order of magnitude CPU time. The model will mostly used united atoms (hydrogens merged into their carbons), but polar hydrogens are treated explicitly. There are lots of parameters and unfamiliar terms in the documentation. Either ignore them or if there is time ask what they mean. The MD calculations will use a time step of 0.002 ps (2×10-15s). You have to know this when labelling the x-axis on the plots. Each 500 steps is 1?ps. The steps will be * convert files to gromacs format * run an energy minimisation * run a very short MD simulation for equilibration and not analyse anything * run a longer simulation in the batch queue and go home * do some analysis of the runs and exchange results with people who worked at different temperatures I