MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg4Print level0 Default: Only eigenvalues are printed in the .log file.Eigenvalues and eigenvectors are printed in the .log file. Note that printing of eigenvectorsgenerates copious output. This is only recommended as a debugging tool.arg5Amplitude (Å)Distance the fastest-moving atom will move in the first N frames. Note that this hasthe same definition as the step size in LMCS.0 1.0 (default).>0 Use this value instead of the default.VBR2 — visualize ViBRational modes, 2nd versionThis command allows for the visualization of molecular vibrations. A file is created which canbe read by the ePlayer facility in Maestro. See Section 8.6 of the Maestro User Manual forinstructions on using the ePlayer. For each mode in the file, the minimized structure comesfirst; then there are some number of frames (call it N) exploring the mode in one direction, 2Nframes exploring it back in the other direction, and finally N additional frames exploring it“forward” again. Each mode is depicted in a different color (up to five). The trivial modes(determined by frequency, not counting) are skipped.VBR2 is virtually identical to the VIBR command, but VBR2 uses ARPACK and can be appliedto a molecule of any size. There are two small differences:• The default amplitude is set to 5 Å in VBR2 in arg5 instead of 1 Å.• VBR2 also uses arg6, to specify a minimum eigenvalue, below which modes are consideredto be trivial (ro-translational) and they are ignored.arg1First mode to animate0 1 (default). Animate starting with the first mode.narg2For n>0, use this value as the first mode to animate instead of the default. Animatestarting with the nth mode.Last mode to animate0 Only the mode specified by arg1 will be animated.58MacroModel 9.7 Reference Manual