Notebooks by Tag

• analysis

  • Analyzing Energy Contributions

• application layer

  • Analyzing Energy Contributions
  • Applying a Constant External Force
  • Changing Temperature and Pressure
  • first_simulation

• barostat

  • Changing Temperature and Pressure
  • first_simulation

• constraints

  • Constraining Atom Positions

• force field

  • Querying and Modifying Charges and Other Parameters

• forces

  • Analyzing Energy Contributions
  • Applying a Constant 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

• restraints

  • Restraining Atom Positions
  • Restraining Dihedrals

• thermostat

  • Changing Temperature and Pressure
  • first_simulation

• topology

  • Merging Molecules

• tutorial

  • Alchemical_free_energy_calculations
  • Beta_2_adrenergic_receptor_B2AR_membrane_protein_simulation_with_CHARMM
  • HSP90_with_ADPMg2_simulation
  • Histone_methyltransferase_simulation_with_a_multisite_water_model_TIP4P-Ew
  • Histone_methyltransferase_simulation_with_multisite_Zn2_structural_ions
  • protein_in_water

• untagged

  • Adding Hydrogens to Nonstandard Molecules
  • Computing Interaction Energies
  • Saving Systems to XML Files
  • Running_a_REST_simulation
  • umbrella_sampling