MacroModel Reference Manual - ISP

Chapter 4: Operation Codes1 Do not perform this test (required for improper torsions).4.12 Free-Energy PerturbationSee Chapter 15 of the MacroModel User Manual for an extended discussion, including adescriptive example.FEGA — Free Energy mutating Group AtomThis command allows explicit addition to the list of atoms whose parameters change during afree-energy perturbation simulation. It is rarely used, since ordinarily the free-energy perturbationgroup atoms are taken to be those atoms that change atom type between the starting andfinal structure, together with any atoms bonded to them. This command could be used to add tothis list, in the event, for example, that the parameters of an atom beta to an atom undergoingmutation changed greatly due to the alteration of the mutating atom.Any FEGA commands must precede all other free-energy perturbation commands.arg1-4Atom numbers0 Add this atom to the mutating atom group.FEIA — Free Energy Interaction Array generationGenerate the two interaction arrays for averaging. It is assumed that the input file contains twostructure files which represent the starting and end points for the mutation. It is furtherassumed that these structures have the same number and ordering of all atoms. Dummy atoms(MacroModel type Du) should be used as counterparts for atoms which disappear or appearduring the simulation.All constraints (FXAT, FXDI, etc.) must be specified before FEIA if the constraints are to beactive during the free-energy perturbation run.FEAV — Free Energy AVeragingThis command, together with FESA, ordinarily appears in a BGIN/END loop that sets up thesimulation for each window in turn. The first time this command is encountered, the interactionarray is generated with the value of lambda given by arg5. You would specify a nonzero valuefor arg5 in order to simulate some individual window, only, or to start a series of windows withsome nonzero value of lambda. This might be useful, for example, if the computer crashed partway through an earlier simulation attempt. It is also used in network-distributed processing toinstruct a given processor to run a simulation over only a single window.MacroModel 9.7 Reference Manual 135