MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1Averaging protocol0 Altered parts of interaction arrays will be averaged.1 Intragroup interactions (see FEGA command) will be zeroed in the final interactionarray (used primarily for testing).arg5Coupling factor (λ) for the current windowThis is the fraction of structure 2 (the mutation end point, the second structure in theinput file) mixed into the molecular representation in the current window.FESA — Free Energy SAmplingSampling protocol for a particular perturbation window. A maximum of 100 FESA commands(defining up to 100 free-energy perturbation windows) can be used. FESA is normally usedwithin a BGIN/END loop to carry out the entire mutation. Arg7 and arg8 can be used to allowautomatic extension of simulation time in a given window to improve convergence.arg2Maximum allowed number of step doublingsSimulation time (MDYN, MCSD) or number of steps (Monte Carlo) can be successivelydoubled to achieve user-defined convergence criteria. This argument allowscontrol over this. See also arg7, arg8.0 2, if arg7 or arg8 are nonzero.arg5arg6arg7Control of double-wide sampling—left halfFraction of structure 1 for the left half of the double-wide sample. If arg5 is equal tothe current window’s value of λ, then no left sampling is done.Control of double-wide sampling—right halfFraction of structure 1 for the right half of the double-wide sample. If arg6 is equalto the current window’s value of λ, then no right sampling is done.Minimum allowed standard deviation (kJ/mol)If the standard deviation of the free-energy difference for this window exceeds thisvalue at end of the simulation, the simulation is doubled in length, in an attempt toimprove the statistical uncertainty in the calculated free energy. A maximum of arg2such doublings are allowed. By default, this option is off.136MacroModel 9.7 Reference Manual