Monitor commands: Commands to monitor various dynamics properties * Menu: * Syntax:: Syntax of the Monitor commands * Properties:: Description of the properties monitored

Syntax of the MONItor commands MONItor {DIHEdral} [SHOW] FIRSt unit-number NUNIt integer BEGIn integer - STOP integer SKIP integer [SELEct atom-selection] FIRSt the unit number of the first file of dynamics coordinate sets from which the property is to be calculated. NUNIt the number of units of dynamics coordinate files. Fortran unit numbers must be assigned to the files consecutively from FIRST. BEGIn the first step number for the coordinate set from which the property will be calculated. STOP the last step number for the coordinate set from which the property will be calculated. SKIP the time increment between the step numbers of the coordinates. SELEct selected atoms for which the property is to be monitored. At this time, atoms may be selected only by the atom-selection keywords (e.g. RESID,TYPE,ATOM,RESN,SEGID) and NOT by tag-selections. (see *note select:(select.doc).) DIHE Property: monitor the dihedral transitions. SHOW for monitoring dihedral transitions, print out the step number, the cumulative number of transitions, the dihedral name, the current dihedral angle, and the old and new minimum well positions each time a transition is found. ALL Lots of printout. UNIT Unit number to write results (default: outu)

Properties monitored using the MONItor commands DIHE: Dihedral transitions are monitored for any dihedral angle which can be made from the atoms selected. A transition is defined as a change in the dihedral angle which results in going from one well of the torsion potential to another well, AND which involves crossing at least 30 degrees beyond the barrier at the potential maximum. That is, for rotation about a bond between tetrahedral carbons, the minima are at +60, 180 and -60, while the maxima are at 0, +120 and -120. For an initial angle of +45, a transition is counted if the angle becomes > +150 or < -30. The old minimum was +60, and the new minima would be 180 or -60, respectively. The angle can change by as much as 120 degrees or as little as 60 degrees in going from one well to the next using this algorithm. For bonded atoms which both have trigonal geometry, the minima are +90 and -90, and a transition requires crossing 0 +- 30, or 180 +- 30 degrees. Only transitions for dihedrals with either 2 or 3 periodicity can be counted with the MONIt command. A word of caution: the above algorithm for counting transitions is by no means fool proof, therefore one should always look at the dihedral time series to obtain a more precise number of transitions. This is particularly true for mainchain phi and psi dihedrals which frequently have average positions which are not close to the minima for a tetrahedral atom. Large fluctuations can therefore be mistakenly (in a classical butane-type transition) counted as transitions.

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Modified, updated and generalized by C.L. Brooks, III

The Scripps Research Institute