DEFINE_ALCHEMICAL_ATOM

NAME
DEFINE_ALCHEMICAL_ATOM

SYNOPSIS
DEFINE_ALCHEMICAL_ATOM  iat1    iat2 on/off

DESCRIPTION
Define an alchemical segment for the solute (N.B. Only solute atoms can be of alchemical types). iat1 and iat3 are the index of the first and last atom of the alchemical segment Alchemical segments can either be switched on or switched off. The alchemical atoms must be part of the starting PDB file whether they interact of not with the actual atoms. This command is used along with the command STEER_PATH ALCHEMY (to define the time protocol of the transformation) and the command PLOT ALCHMEY (to printing out the work done during the transformation).

EXAMPLES

• Example 1.
  DEFINE_ALCHEMICAL_ATOM 1 10 on
  ... STEER_PATH ALCHEMY alchemy.time.on
  

  atoms from 1 to 10 of the solute will be switched on with a time protocol specified in the file alchemy.time.on

• Example 2.
  

  DEFINE_ALCHEMICAL_ATOM 1 10 off
  ... STEER_PATH ALCHEMY alchemy.time.off
  

  atoms from 1 to 10 of the solute will be switched off with a time protocol specified in the file alchemy.time.off

• Example 3.
  DEFINE_ALCHEMICAL_ATOM 1 10 on
  DEFINE_ALCHEMICAL_ATOM 10 20 off
  ... STEER_PATH ALCHEMY alchemy.time.on.off
  

  atoms from 1 to 10 of the solute will be switched on and atoms from 10 to 20 of the solute will be switched off each with a time protocol specified in the common file alchemy.time.on.off