Contents

• Introduction
  • Changes from previous versions
  
  
• Description of the molecular structure and the force field
  • The force field
  • Molecular geometry and non-bonded interaction parameters
  • Bonds
  • Covalent angles
  • Dihedral angles
  • Optional features of the force field
  
  
• The main input file
  • General notes
  • Basic setup
  • Restart control
  • System
  • Ensemble
  • Molecular Dynamics
  • Startup
  • Expanded Ensemble mode
  • Path Integral mode
  • Properties
  
  
• Compilation
  • Sequential execution
  • Parallel execution
  • Other makefiles
  
  
• Execution
  • Files used by the program
  • Memory considerations
  • Program structure
  
  
• Makemol utility
  • General organization
  • The force field (.ff) file
  • The molecular structure (.smol) file
  
  
• Tranal utility
  • General organization
  • tranal_base: reading trajectories
  • Computation of the electron density and electrostatic potential in bilayers: bileldens.f
  • Dielectric constant: diel.f
  • Diffusion: diffus.f
  • Dryrun: dryrun.f
  • Lateral diffusion: latdiff.f
  • Order parameters: order.f
  • Radial distribution functions: rdf.f
  • Spatial distribution functions: sdf.f
  • Distribution of torsion angles: torsion.f
  • Ramachandran plot for a pair of torsion angles: torsion2.f
  • Time correlation functions: trtcf.f