Notebooks by Tag

• analysis

  • Analyzing Energy Contributions

• application layer

  • Analyzing Energy Contributions
  • Applying a Fixed External Force
  • Changing Temperature and Pressure
  • First Simulation
  • Reporting Minimization

• barostat

  • Changing Temperature and Pressure
  • First Simulation
  • Reporting Minimization

• constraints

  • Constraining Atom Positions

• force field

  • Querying and Modifying Charges and Other Parameters

• forces

  • Analyzing Energy Contributions
  • Applying a Fixed External Force
  • Querying and Modifying Charges and Other Parameters
  • Restraining Atom Positions
  • Restraining Dihedrals

• inspection

  • Querying and Modifying Charges and Other Parameters

• modeller

  • Merging Molecules in a Topology

• restraints

  • Restraining Atom Positions
  • Restraining Dihedrals

• thermostat

  • Changing Temperature and Pressure
  • First Simulation
  • Reporting Minimization

• topology

  • Merging Molecules in a Topology

• tutorial

  • Alchemical free energy calculations
  • Beta-2-adrenergic receptor (B2AR) membrane protein simulation with CHARMM
  • HSP90 with ADP:Mg2+ simulation
  • Histone methyltransferase simulation with a multisite water model (TIP4P-Ew)
  • Histone methyltransferase simulation with multisite Zn2+ structural ions

• untagged

  • Adding Hydrogens to Nonstandard Molecules
  • Building Systems from Scratch
  • Coarse-Grained Polymer
  • Computing Interaction Energies
  • Getting Started with OpenMM
  • Loading Input Files and Reporting Results
  • Run a REST simulation
  • Saving Systems to XML Files
  • Selecting Values for Simulation Parameters
  • Simulating Conductive Electrodes with the Constant Potential Method
  • Umbrella Sampling