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Section DEFINE_REGION

Index of all sections. This section is located at __ROOT__%MOTION%MD%REFTRAJ%MSD%DEFINE_REGION.

This section provides the possibility to define arbitrary region for the MSD calculation. This section can be repeated and can not be optional.

Subsections

None

Section keywords

Keyword descriptions

LIST
LIST {integer} {integer} .. {integer}
Specifies a list of atoms to thermostat.
This required keyword expects a list of integers, and may repeat
MOLNAME
MOLNAME WAT MEOH
Specifies the name of the molecules to thermostat
This required keyword expects a list of words, and may repeat
variants: SEGNAME
MM_SUBSYS
MM_SUBSYS (NONE|ATOMIC|MOLECULAR)
In a QM/MM run all MM atoms are specified as a whole ensemble to be thermostated
This required keyword expects a keyword. Default value: NONE
valid keywords:
  • NONE: Thermostat nothing
  • ATOMIC: Only the MM atoms itself
  • MOLECULAR: The full molecule/residue that contains a MM atom
variants: PROTEIN
QM_SUBSYS
QM_SUBSYS (NONE|ATOMIC|MOLECULAR)
In a QM/MM run all QM atoms are specified as a whole ensemble to be thermostated
This required keyword expects a keyword. Default value: NONE
valid keywords:
  • NONE: Thermostat nothing
  • ATOMIC: Only the QM atoms itself
  • MOLECULAR: The full molecule/residue that contains a QM atom


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