PLUMED-NEST

Project ID: plumID:23.036
Source: aq/plumed.dat
Originally used with PLUMED version: 2.8.1
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

#spib_learned_cv
#
#RESTART
  
q6: 
Q6
Calculate sixth order Steinhardt parameters. More details
 
R_0
The r_0 parameter of the switching function
=0.33 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

The Q6 action with label q6 calculates somethingq4: 
Q4
Calculate fourth order Steinhardt parameters. More details
 
R_0
The r_0 parameter of the switching function
=0.33 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility


The Q4 action with label q4 calculates somethingene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingvol: 
VOLUME
Calculate the volume of the simulation box. More details


The VOLUME action with label vol calculates the volume of simulation box
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=enthalpy
 
ARG
the input to this function
=ene,vol
 
COEFFICIENTS
 the coefficients of the arguments in your function
=1.0,0.060221409
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

The COMBINE action with label enthalpy calculates something
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h
 
ARG
the input to this function
=enthalpy
 
POWERS
 the powers to which you are raising each of the arguments in your function
=1
 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.00926
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE


The COMBINE action with label h calculates something
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 ...
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.33 D_MAX=0.6}
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512
MEAN
 calculate the mean of all the quantities
MOMENTS
the list of moments that you would like to calculate
=2
MORE_THAN1
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=4.0}
MORE_THAN2
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=5.0}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

The COORDINATIONNUMBER action with label cn calculates somethingcv1_l: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.676064,-0.720446,-1.56094,0.706886,-0.030074,-0.0025326,6.20144e-05 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label cv1_l calculates somethingcv2_l: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h 
COEFFICIENTS
 the coefficients of the arguments in your function
=-2.00895,1.89549,-3.15277,-0.432,0.00841427,0.0416259,-0.00289463 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label cv2_l calculates somethingcv1: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cv1_l 
FUNC
the function you wish to evaluate
=x+2.809855 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 

The MATHEVAL action with label cv1 calculates somethingcv2: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cv2_l 
FUNC
the function you wish to evaluate
=x-3.756015 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The MATHEVAL action with label cv2 calculates somethingmetad: 
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,cv2 
SIGMA
the widths of the Gaussian hills
=0.15,0.24 
HEIGHT
the heights of the Gaussian hills
=5 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
GRID_MIN
the lower bounds for the grid
=-4.5,-7 
GRID_MAX
the upper bounds for the grid
=3,5 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cv1,cv2,q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h,metad.bias,metad.rbias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=100