Running Molecular Dynamics on Alliance clusters with AMBER: Glossary

Key Points

An Overview of Information Flow in AMBER

  • To run an MD simulation with AMBER 3 files are needed: an input file, a parameter file, and a file describing coordinates/velocities .
Checking and Preparing PDB Files

  • Small errors in the input structure may cause MD simulations to became unstable or give unrealistic results.
Assigning Protonation States to Residues in a Protein

  • Assigning correct protonation states of aminoacids in proteins is crucial for realistic MD simulations

  • Conformational changes in proteins may be accompanied by changes in protonation pattern.
Solvating a System, Adding Ions and Generating Input Files

  • Simulation system must be neutralized by adding counter-ions to obtain the correct electrostatic energy.

  • Ions are added to a simulations system to mimic composition of a local macromolecule environment.

  • Solvent box should be large enough to allow for unrestricted conformational dynamics of a macromolecule.
Running Molecular Dynamics Simulations with AMBER
Preparation and simulation of membrane and membrane-protein systems
Hands-on 1: Packing a complex mixture of different lipid species into a bilayer and simulating it
Hands-on 2: Transferring AMBER simulation to GROMACS
Hands-on 3A: Preparing a Complex RNA-protein System

  • ?
Hands-on 3B: Simulating a Complex RNA-protein System
Hands-on 4: Preparing a system for simulation with GROMACS
Hands-on 5: Generating topologies and parameters for small molecules.
Hands-on 6: A Comparative Performance Ranking of the Molecular Dynamics Software

  • To assess CPU efficiency, you need to know how fast a serial simulation runs

Glossary

FIXME

barostat
Pressure control algorithms in molecular dynamics (MD) simulations are commonly referred to as barostats and are needed to study isobaric systems. Barostats work by altering the size of the simulation box. Therefore they can only be used in conjunction with periodic boundary conditions (PBC).
ergodicity
In statistical mechanics ergodicity describes the principle that studying a single particle averaged over a long time is equivalent to averaging over many particles which are studied for a short time. See also: “Ergodicity” on Wikipedia
periodic boundary conditions
Periodic boundary conditions (PBC) … See also:
thermostat
Temperature control algorithms in molecular dynamics (MD) simulations are commonly referred to as thermostats and are needed to study isothermal systems. Thermostats work by altering the velocities of particles.

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