Alchex Methodology

Configuring Alchex

1. Parameter Files .itp and Reference Structures .gro are added to a residue library.
2. Exchange Mappings between parameter files are calculated

Using Alchex

Once configured Alchex requires:

• input structure in .gro format
• input topology in .top format along with all included .itp files. This should include parameters for both the source and destination residues.
• Replacement Specification

Alchex can additionally been provided with:

• Additional em parameters in .mdp format.
• Additional alchembed parameters in .mdp format.

Alchex methodology

• Input structure is loaded.
• Exchangable Entities (may contain several residues) are created and assigned a destination molecule.
• Groups of entities are calculated such that groups do not share neighbours.
• Atoms of each group are replaced.
• Each group is energy minimised.
• Each group is alchemically replaced into the original simulation.