MacroModel Reference Manual - ISP

Chapter 4: Operation CodesnWrite every nth structure sampled.SRNO — SeRial Number Orderingarg1Number to be added to serial number property in output structure file4.11 Molecular Dynamics and Monte Carlo SimulationsMDYN — Molecular DYNamicsCarry out molecular dynamics. Structures must be fully minimized before molecular dynamicsis initiated and initial conditions (temperature, time step, and total time) must be selected.Temperature maintenance with a constant temperature bath is recommended. If too high atemperature or too large a time step is selected, the structure will eventually gain too muchkinetic energy and blow up (program automatically aborts if the kinetic energy/atom exceeds100 kJ/mol). The structure may also blow up if it is not sufficiently minimized and energy isadded (e.g., MDIT). If this occurs, reduce the time step, turn on SHAKE (arg 2) and try again.During the run, average temperatures (both over the most recent 0.5 ps and over the entiresimulation so far), the instantaneous total energy (potential plus kinetic energy) and theaverage enthalpy over the entire simulation (taken as the average steric energy) are written tothe log file. If you choose the full printing option (arg1=2), the information is written to the.mmo file as well. If you are using constant energy molecular dynamics (no temperaturecontrol), the energy may change over the course of the simulation: if the temperature listedafter 0.5 ps or so is more than 5% too high, then it is likely that the starting geometry was notcompletely minimized or that a lower energy nearby minimum has been found.If you are not using temperature control and wish to readjust the temperature, stop the batchjob and set the desired temperature with arg 7. Start the run again and the temperature willadjust itself over the first several ps.It is best to do the simulation in stages (e.g., to begin by equilibrating the system prior theactual run) having a MDYN command for each stage. If the MDRE (reset) command is not used,the run will continue from the previous end point. Equilibration runs are suggested for goodthermodynamics especially if there is no reason to believe that the starting structure is the fullyminimized global minimum. We suggest at least 5-50 ps of equilibration before data collectionfor all molecular dynamics operations other than conformation searching where equilibrationis unnecessary. Experience shows that ca .2-.5 times the number of heavy atoms gives a reasonableequilibration time in picoseconds.The time step (in femtoseconds (Default = 1.5 fs), arg5) is the time interval of each step of themolecular dynamics run. Energy stability is best at or below 1.0 fs but time steps up to 2.5 fsmay be used to reduce the overall time required for the simulation. If too large a time step isMacroModel 9.7 Reference Manual 117