MacroModel Reference Manual - ISP

Chapter 4: Operation Codesment. We recommend using the default behavior, and making manual adjustmentsto TORS and MOLS if acceptance is too high or low.MDVE — Molecular Dynamics VElocity fileThis command directs MacroModel to write or read a velocity file to or from disk. The file hasdouble precision x,y,z velocities for each atom. The filename is out-filename.vel whenwriting a velocity file and in-filename.vel when reading one. This option is useful for listingthe velocities, for saving the velocities to continue a molecular dynamics run at some later timeand as a mechanism by which externally generated velocities may be used as moleculardynamics starting points. Velocity files are stored as formatted disk files. Each line containsx,y,z velocities (meters/sec) for each substructure atom. The Fortran format for each line in thevelocity data in the file is (3D20.12).A velocity file read (arg1=1) must come after READ or SUBS commands and before any MDYNcommand. A velocity file write (arg1=0) must come after the MDYN command.MDYN does not write final structures to the output file unless the WRIT command follows it. Wegenerally save both final velocities and structures at the end of a molecular dynamics run.arg 1Read/write a velocity file0 Write file.1 Read file.MDFR — Molecular Dynamics update FRequencySets the frequency in picoseconds for updates of the nonbonded array.For molecules where large movements of groups are expected, the nonbonded array should beperiodically updated (e.g., every 0.2-0.5 ps). A better alternative is to use very long cutoffs(using EXNB command) and a force field like OPLS, which does not have explicit hydrogenbonding potentials. The more frequently the nonbonded array is updated, the slower thedynamics will run.arg5Update interval (fs) (default: do no updates)MDRE — Molecular Dynamics REsetReset or reinitialize all molecular dynamics variables, set initial velocities to zero.MacroModel 9.7 Reference Manual 129