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Molecular Modeling Practical

This tutorial introduces the student to the practice of Molecular Dynamics (MD) simulations of proteins. The protocol used is a suitable starting point for investigation of proteins, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information.

Practical Report

Each group should hand in only one report. The group number and the names of the group members should be on the first page. The report should start with a short introduction of what was the purpose of the work and contain the following elements:

  • A table containing information about the MD simulations:
    • Protein
    • Number of amino acids
    • Number of protein atoms
    • System volume
    • Number of solvent molecules
    • Total number of atoms
    • Simulation length

Answers to the questions below.
These questions correspond to the questions given during the tutorial and can be used as a check list. Rephrase each question in your answer, but try to keep answers concise; use one or two sentences per question. Answers may be found in the input parameter files, in the output or in the online manual of Gromacs


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