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# monitor (c41b1)

Monitor commands: Commands to monitor various dynamics properties

* Syntax | Syntax of the Monitor commands

* Properties | Description of the properties monitored

* Syntax | Syntax of the Monitor commands

* Properties | Description of the properties monitored

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[SYNTAX MONItor dihedral transitions]

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. (

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)

[SYNTAX MONItor dihedral transitions]

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. (

**»**select .)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)

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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.

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.