Project ID: plumID:19.082
Source: Ammonia_borane/4.H2_release/AaDB/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.9
tested onmaster
RESTART
Activate restart. More details
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
h:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=5-128:16,6-128:16,7-128:16,8-128:16,9-128:16,10-128:16,11-128:16,12-128:16,13-128:16,14-128:16,15-128:16,16-128:16 hb:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=7-128:16,8-128:16,13-128:16,14-128:16,15-128:16,16-128:16 hn:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=5-128:16,6-128:16,9-128:16,10-128:16,11-128:16,12-128:16 n:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=3-128:16,4-128:16 b:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=1-128:16,2-128:16 bn1:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=1-128:16,3-128:16 bn2:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=2-128:16,4-128:16
cnHB:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=hb
SPECIESB
this keyword is used for colvars such as the coordination number
=b
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.8 NN=6 MM=12}
MAX
calculate the maximum value
={BETA=0.02} cnHH:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=hn
SPECIESB
this keyword is used for colvars such as the coordination number
=hb
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN R_0=0.2 D_0=0.8 }
MAX
calculate the maximum value
={BETA=0.02}
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
ARG
the input for this action is the scalar output from one or more other actions
=cnHH.max
FILE
the name of the file containing the external potential
=ext_bias.dat
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external
METAD
Used to performed metadynamics on one or more collective variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=cnHH.max
SIGMA
the widths of the Gaussian hills
=0.05
HEIGHT
the heights of the Gaussian hills
=0.1
PACE
the frequency for hill addition
=4000
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=400
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
STRIDE
the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=COLVAR
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
STRIDE
the frequency with which all the open files should be flushed
=1
ENDPLUMED
Terminate plumed input. More details