Welcome to GOMC’s documentation!

Contents:

• Overview
• Release 2.75 Notes
• Introduction
  • GOMC supported ensembles:
  • GOMC supported Monte Carlo moves:
  • GOMC supported force fields:
  • GOMC supported molecules:
• Software Requirements
  • C++11 Compliant Compiler
  • CMake
  • CUDA Toolkit
  • MPI (Optional for Standard; Required for MultiSim)
• Recommended Software Tools
  • Packmol
  • VMD
  • Molecular Simulation Design Framework (MoSDeF)
• How to get the software
  • GitHub
  • Website
• Compiling GOMC
  • Linux
  • Windows
  • Configuring CMake
• GPU-Accelerated GOMC
• Input File Formats
  • PDB File
  • PSF File
  • Topology File
  • Parameter File
  • Exotic or Mie Parameter File
  • Control File (*.conf)
  • Binary input file types
• GOMC’s Output Files
  • Console Output
  • Block Output Files
  • PDB Output Files
  • PSF Output File
  • Molecule Distribution Output File
  • Histogram Output File
  • Free Energy Output File
  • Checkpoint Output File
• Putting it all together: Running a GOMC Simulation
• Intermolecular Energy and Virial Function (Van der Waals)
  • VDW
  • EXP6
  • SHIFT
  • SWITCH
  • SWITCH (MARTINI)
• Intermolecular Energy and Virial Function (Electrostatic)
  • Ewald
  • VDW
  • EXP6
  • SHIFT
  • SWITCH
  • SWITCH (MARTINI)
• Long-range Correction (Energy and Virial)
  • VDW
  • EXP6
• Coupling Interaction with \(\lambda\)
  • VDW
  • Electrostatic
  • Long-range Correction (VDW)
  • Long-range Correction (Electrostatic)
• Hybrid Monte Carlo-Molecular Dynamics (MCMD)
  • GOMC Requirements
  • NAMD Requirements
  • Dynamic Subvolumes for Dual Control Volume Molecular Dynamics
  • Run a Hybrid Monte Carlo-Molecular Dynamics Sim
• How to?
  • Visualizing Simulation
  • Build molecule and topology file
  • Simulate rigid molecule
  • Restart the simulation
  • Recalculate the energy
  • Simulate adsorption
  • Calculate Solvation Free Energy
  • Run a Multi-Sim
  • Simulate a protein as a fixed body
• Get Help or Technical Support