MacroModel Reference Manual - ISP

Chapter 4: Operation CodesMDAV — Molecular Dynamics coordinate AVeragingAveraging of atomic Cartesian coordinates during the molecular dynamics run. The averageatomic coordinates will be used as the structure coordinates at the end of the dynamics run.The coordinates will be written to the output structure file. To save these coordinates in theoutput file, it is necessary to use a WRIT command after the MDYN command.This command must precede the MDYN run to be averaged.arg1Control0 Perform no averaging.1 Perform averaging.MDIT — Molecular Dynamics Initial TemperatureInitial Temperature (K, Absolute) for the start of the run. This temperature is converted to thecorresponding kinetic energy, and that energy is used to initialize the velocities of all atoms. Arandom Gaussian distribution of velocities is generated such that the total energy is distributedequally along the three Cartesian axes. 3RT is also supplied for translation/rotation for eachmolecule beyond the first. The total energy added is (3N-6M)*RT (M is the number of translation/rotationconstraints, normally 1). Note that the MDIT command replaces any current velocitieswith random new ones and assumes that the structure is completely minimized (if it is not,the resulting temperature will be higher than that given in this command unless temperaturecontrol is used).If no initial temperature is specified, the simulation keeps the kinetic energy from a previousrun. If a structure is fully minimized and no initial temperature (or initial energy) is specified,the simulation will not run. If a structure is not fully minimized, the difference between thecurrent strain energy and the minimum energy builds up in the kinetic energy term.The standard dynamics protocol is to fully minimize a structure, then start the simulation eitherwith the desired temperature, or slowly increase the kinetic energy (set an initial (MDIT) andwarm the molecule over ca 5 ps (MDYN args 7 and 8)) prior to an equilibration run. If an equilibrationperiod is used, the actual run will occur in a separate step without specification of newinitial or final temperatures.If a precise (harmonic) temperature is desired, use the MDYN arg7 to set constant temperaturedynamics. This will insure that the final temperature attained will be that desired regardless ofthe relative energy of the starting structure and any nearby (local) minima after equilibration.arg5Temperature (K)126MacroModel 9.7 Reference Manual