Project ID: plumID:19.082
Source: Ammonia_borane/2.AaDB_to_AB2/AaDB_bis/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
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 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 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 bm2:
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
=1-128:16,18-128:16 nm4:
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
=3-128:16,20-128:16
bbinter:
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
=2
SPECIESB
this keyword is used for colvars such as the coordination number
=bm2
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=2.5 NN=6 MM=12}
MEAN
calculate the mean of all the quantities
nninter:
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
=4
SPECIESB
this keyword is used for colvars such as the coordination number
=nm4
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=2.5 NN=7 MM=14}
MEAN
calculate the mean of all the quantities
bhbridge:
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
R_0
The r_0 parameter of the switching function
=1.9
NN
The n parameter of the switching function
=6
MM
The m parameter of the switching function; 0 implies 2*NN
=12
MAX
calculate the maximum value
={BETA=0.02} nhbridge:
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
=n
R_0
The r_0 parameter of the switching function
=1.6
NN
The n parameter of the switching function
=6
MM
The m parameter of the switching function; 0 implies 2*NN
=12
MAX
calculate the maximum value
={BETA=0.02} nhcoord:
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
=4
SPECIESB
this keyword is used for colvars such as the coordination number
=hn
R_0
The r_0 parameter of the switching function
=1.6
NN
The n parameter of the switching function
=7
MM
The m parameter of the switching function; 0 implies 2*NN
=14
MEAN
calculate the mean of all the quantities
bhcoord:
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
=2
SPECIESB
this keyword is used for colvars such as the coordination number
=hb
R_0
The r_0 parameter of the switching function
=1.8
NN
The n parameter of the switching function
=7
MM
The m parameter of the switching function; 0 implies 2*NN
=14
MEAN
calculate the mean of all the quantities

d1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bbinter.mean
COEFFICIENTS
the coefficients of the arguments in your function
=0.8107
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=nninter.mean
COEFFICIENTS
the coefficients of the arguments in your function
=1.1786
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d3:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bhbridge.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.4960
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d4:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=nhbridge.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.6050
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d5:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=nhcoord.mean
COEFFICIENTS
the coefficients of the arguments in your function
=0.2545
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d6:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bhcoord.mean
COEFFICIENTS
the coefficients of the arguments in your function
=0.2388
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
sdg1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6
COEFFICIENTS
the coefficients of the arguments in your function
=-0.0481,-0.0473,-0.1976,-0.2464,0.9415,0.0959
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO sdg2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6
COEFFICIENTS
the coefficients of the arguments in your function
=0.6319,-0.0329,-0.2130,-0.0029,0.4767,-0.5719
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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
=sdg1,sdg2
SIGMA
the widths of the Gaussian hills
=0.03,0.03
HEIGHT
the heights of the Gaussian hills
=1.5
PACE
the frequency for hill addition
=100
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
=8
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
WALKERS_N
number of walkers
=4
WALKERS_ID
walker id
=1
WALKERS_DIR
shared directory with the hills files from all the walkers
WALKERS_RSTRIDE
stride for reading hills files
=50 ... METAD
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