DEFINE_REGION

Section can be repeated.

Define arbitrary thermal region with distinct temperature controls. For thermostat regions, see section MOTION%MD%THERMOSTAT%DEFINE_REGION; when the keyword MOTION%MD%THERMOSTAT%REGION is set to THERMAL, the definition of thermostat regions will be the same as that of thermal regions. [Edit on GitHub]

Subsections

TFUNC

Keyword descriptions

DO_LANGEVIN

Type: logical
Default: T
Lone keyword: T
Usage: DO_LANGEVIN .TRUE.

Description: When ENSEMBLE is set to LANGEVIN, Controls whether the atoms in the thermal region should undergo Langevin MD. If not, then they will undergo NVE Born-Oppenheimer MD.

Mentions: ⭐Langevin Dynamics

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LIST

Type: integer[ ]
Repeatable: yes
Usage: LIST {integer} {integer} .. {integer}

Description: Specifies a list of atoms belonging to the region.

Mentions: ⭐Langevin Dynamics

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MM_SUBSYS

Type: enum
Default: NONE
Aliases: PROTEIN
Usage: MM_SUBSYS (NONE|ATOMIC|MOLECULAR)

Description: Not yet implemented: In a QM/MM run all MM atoms are specified as a whole region

Valid values:

NONE Nothing in the region
ATOMIC Only the MM atoms itself
MOLECULAR The full molecule/residue that contains a MM atom

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MOLNAME

Type: string[ ]
Repeatable: yes
Aliases: SEGNAME
Usage: MOLNAME WAT MEOH

Description: Specifies the name of the molecules belonging to the region.

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NOISY_GAMMA_REGION

Type: real
Default: [fs^-1]
Usage: NOISY_GAMMA_REGION 4.0E-5

Description: Special imaginary Langevin Friction term for Langevin Dynamics with noisy forces for the atoms in this region. When set, overrides the general value set by NOISY_GAMMA in the MOTION%MD%LANGEVIN section. When unset for a defined region, the general NOISY_GAMMA value applies.

References: Kühne2007

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QM_SUBSYS

Type: enum
Default: NONE
Usage: QM_SUBSYS (NONE|ATOMIC|MOLECULAR)

Description: Not yet implemented: In a QM/MM run all QM atoms are specified as a whole region

Valid values:

NONE Nothing in the region
ATOMIC Only the QM atoms itself
MOLECULAR The full molecule/residue that contains a QM atom

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TEMPERATURE

Type: real
Default: 0.00000000E+000 [K]
Usage: TEMPERATURE 5.0

Description: The temperature in K used to initialize the velocities of the atoms in this region. It overrides the value evaluated by the function defined in TFUNC section.

Mentions: ⭐Langevin Dynamics

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TEMP_TOL

Type: real
Default: 0.00000000E+000 [K]
Usage: TEMP_TOL 0.0

Description: Maximum accepted temperature deviation from the target value for this region, which is defined by TEMPERATURE or evaluated with the function defined in TFUNC section. Default value is 0 that turns off rescaling.

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