Welcome to AlchemicalITP’s documentation!

AlchemicalITP is a library for modifying the Gromacs topology file for performing alchemical transformations.

Contents:

• Generation of topology file for FEP calculations
  • Input Coordinate and Topology
  • Mapping between state A and state B
  • For Splitting the Transformation into Three Parts
  • Validation of the Generated Topology
• Rules in Making the Transformation
  • Atomtypes
  • Atoms
  • Bonded interactions
  • cmap
• Sequential Transformation
  • Atoms being Annihilated
  • Growth of Atoms
  • Three-steps Transformation
• Generation of topology file for ABFE calculations
  • Problem with the ordinary ABFE calculations
  • The restraint and charge annihilation
  • The decoupling of van der waals

Indices and tables

• Index

• Module Index

• Search Page