MacroModel Reference Manual - ISP

Chapter 4: Operation CodesMDAP — Molecular Dynamics Atom Position monitoringAtom Position monitoring during the molecular dynamics run. Output consists of average rmsdeviation (Å) from original position. The output is written to the log and .mmo output file.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.Note:arg1-4This command must precede the MDYN command to be monitored.Atom numbers for position monitoringMDDI — Molecular Dynamics DIstance monitoringDistance monitoring during a molecular dynamics run. Output consists of histogram-likecompilations of internuclear distances/frequencies and the average distance. Histograms have100 bins covering the range of arg6 to arg6+arg5*100. The default range is 0–10 Å in 0.1 Åincrements. The output is written to the .mmo output file.Data is accumulated every 10 time steps throughout the simulation and also when the structureis sampled. DEBG 1 lists each value to the log file. A maximum of 100 distances may be monitoredsimultaneously.This command must precede the MDYN command for monitoring to take place.arg1First atom of pair0 No distances monitored.>0 First atom of pair.arg2arg5Second atom of pairBin width for histogramsWidth of bins for distance monitoring in angstroms. The default value is 0.1 Å, andthe minimum value is 0.01 Å.0 Use the default value of 0.1 Å.>0 Use this value.arg6Lower limit of histogram rangeSmallest distance value recorded in the histogram, in angstroms. Default: 0 Å.MacroModel 9.7 Reference Manual 123