MacroModel Reference Manual - ISP

Chapter 4: Operation CodesMDMT — Molecular Dynamics MomenTum resetUsed to control translational and rotational (angular) momentum which will be periodically(0.1 ps by default) reset to zero. MDMT is operational by default (i.e., MDMT is unnecessary unlessit has previously been turned off), and its normal mode is constraint of the total molecularsystem to have zero translational momentum.Note:Structures viewed graphically will not appear to translate or rotate even if momentumis not zeroed because they are translated/rotated to the original position and overallorientation before writing to any output file.The frequency of momentum zeroing is set by arg 5.arg1Choice of momentum elements to be reset0 No momentum resetting. This is the default for stochastic dynamics.1 Set total translational momentum to zero.2 Set total translational and rotational momentum to zero. This is the default formolecular dynamics.arg5Frequency of momentum resettingDefault: 0.1 ps.MDAR — Molecular Dynamics ARea monitoringAtomic area monitoring during the molecular dynamics run. Output consists of histogram-likecompilations of individual atomic areas and the averages. The output will be written to the mmooutput file. If no probe radius is specified, then the areas will reflect the van der Waals surfaceareas for the atoms specified. If all atoms are to have the same probe radius, use MDARcommands loaded with four atoms at a time using args1-4.Data is accumulated every 10 time steps throughout the simulation and also when the structureis sampled. DEBG switch 1 lists each value to the .log file. A maximum of 250 atoms may bemonitored simultaneously.This command must precede the MDYN command to be monitored.arg1-4Atom numbers for area monitoringarg5 Probe radius (Default: 0)122MacroModel 9.7 Reference Manual