PLUMED-NEST

Project ID: plumID:23.026
Source: plumed_model_2D_WTD.dat
Originally used with PLUMED version: 2.5.2
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

# LOAD FILE=PythonCV.dylib
grp: 
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
=1-421
The GROUP action with label grp calculates somethingcv1: 
PYTHONCV
This action is not part of PLUMED and was included by using a LOAD command More details
 ATOMS=1-421 IMPORT=model_2D FUNCTION=cv1 COMPONENTS=ncl,nq6

cn: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.0 D_MAX=13.0}
### calculate the number of particles with crystalline order (first shell geometries)
The COORDINATIONNUMBER action with label cn calculates somethingq6: 
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The Q6 action with label q6 calculates somethinglq6: 
LOCAL_Q6
Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. More details
 SPECIES=q6 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The LOCAL_Q6 action with label lq6 calculates somethingflq6: 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=lq6 
SWITCH
the switching function that transform
={GAUSSIAN R_0=0.69 D_MAX=0.70}

### calculate the coordination number distributions for these crystalline particles and count them
The MFILTER_MORE action with label flq6 calculates somethingcnq6: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=flq6 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=11.0 D_MAX=13.0}

The COORDINATIONNUMBER action with label cnq6 calculates somethingn: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cn.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=0.33333333 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The COMBINE action with label n calculates somethingnq6: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cnq6.morethan 
POWERS
 the powers to which you are raising each of the arguments in your function
=0.333333 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label nq6 calculates somethinglwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cv1.nq6 
AT
the positions of the wall
=-0.5 
KAPPA
the force constant for the wall
=150.0 
EXP
 the powers for the walls
=4 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0

The LOWER_WALLS action with label lwall calculates somethingres: 
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
=cv1.ncl,cv1.nq6 
SIGMA
the widths of the Gaussian hills
=0.18,0.05 
HEIGHT
the heights of the Gaussian hills
=0.1 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=2 
GRID_MIN
the lower bounds for the grid
=-0.5,-1.5 
GRID_MAX
the upper bounds for the grid
=10,8 
GRID_BIN
the number of bins for the grid
=200,200

The METAD action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=colvar.out 
ARG
the input for this action is the scalar output from one or more other actions
=cv1.ncl,cv1.nq6,res.bias,res.work,cn.morethan,cnq6.morethan 
STRIDE
 the frequency with which the quantities of interest should be output
=500