atomMovability

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Purpose

The atomMovability command is used to set and unset movability characteristics of atoms.

Syntax

atomMovability operation arg1 ?arg2 ...?

Command Operations:


Operation       Arguments      Description


set             type           Set movability characteristic type for the 
                name           atom set specified by spec. The values of 
                spec           type and spec are associated with name for 
                               later reference.

unset           name           Unset movability characteristic for the atom 
                               set associated with name or unset all 
                               movability characteristics if value of name is 
                               -all. When movability characteristic is unset, 
                               it reverts to the default value (movable).

Command Arguments:


Argument        Operation      Description


type          set              Legal values are movable, fixed, and excluded. 
                               Movable atoms participate fully in system
                               motions and interactions. Fixed atoms exert 
                               forces on other atoms, but do not move. 
                               Excluded atoms have no effect on other atoms 
                               and do not move.

name          set/unset        Arbitrary string selected by user.

spec          set              General atom or subset spec.

Description

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Atom movability characteristics specified with the atomMovability command are applied in the order in which they are specified. Thus, an initial movability specification for an atom can be overridden by a subsequent command. Unsetting the subsequent specification restores the effect of the initial command.

The atomMovability command is actually a TCL procedure (defined in $BIOSYM/data/utility/atomMovability.tcl) that employs the set command to store the specification data into TCL associative arrays.

Examples

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These examples show the differences between atom movability exclusion and energy calculation exclusion in calculations. If an atom is excluded using the atomMovability command, all energies (bond, angle, nonbond) involving that atom are excluded. These examples have been combined into an example exclusions.inp file, which you can run by saving it to a directory in which you have write permission and also copying the acenm.car and acenm.mdf files from the $BIOSYM/gifts/discover/tcl directory into the same directory. The exclusions.inp file contains echo statements to help make the examples clearer when the exclusions.inp file is run.

Example 1 - Allow all atoms to move

energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int1 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b1 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a1 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb1 Values.Value $e1

Example 2 - Prevent one atom from moving

atomMovability set excluded ex1 "ACENM:ACE_1:HA1"
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int2 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b2 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a2 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb2 Values.Value $e1
atomMovability unset ex1

If you run this example, note that both the nonbond and internal energies are different.

Example 3 - Exclude the internal energy calculation of one atom

System_SetExcludeInternalEnergy "ACENM:ACE_1:HA1"
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int3 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b3 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a3 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb3 Values.Value $e1
System_SetExcludeInternalEnergy "ACENM:ACE_1:HA1" Include

If you run this example, note that all the energies are the same as in Example 2.

Example 4 - Exclude the internal energy calculation of two atoms

System_SetExcludeInternalEnergy "ACENM:ACE_1:(CA,HA1)"
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int4 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b4 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a4 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb4 Values.Value $e1
System_SetExcludeInternalEnergy "ACENM:ACE_1:(CA,HA1)" Include

If you run this example, note that the nonbond energy is unchanged but the internal energy is changed. Also note that the bond energy is now the same as that in Example 1.

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