PLUMED-NEST

Project ID: plumID:21.041
Source: 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

# PLUMED works internally in kJ/nm/ps if no UNITS command is used in PLUMED input file
u_cnThe COORDINATION action with label u_cn calculates the following quantities:
 Quantity   
 Type   
 Description  
u_cn
scalar
the value of the coordination:     COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1-256 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=257-512 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 D_0 The d_0 parameter of the switching function=0.13 R_0The r_0 parameter of the switching function=0.21 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5000
u_volThe VOLUME action with label u_vol calculates the following quantities:
 Quantity   
 Type   
 Description  
u_vol
scalar
the volume of simulation box:    VOLUMECalculate the volume the simulation box. More details

## Two different ions groups are distinguished by their ID e.g (1-256) for Na+ ions and (257 - 512) for Cl- ions

cnThe COMBINE action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
scalar
a linear compbination:       COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=u_cn     COEFFICIENTS the coefficients of the arguments in your function=0.003906250000 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Number 0.003906250000 equals to 2.0/512, where 512 stands for the system size.
# The number is the prefactor for the average coordination number (see Eq. (1) in Phys. Rev. Let. 127, 105701 (2021))

volumeThe COMBINE action with label volume calculates the following quantities:
 Quantity   
 Type   
 Description  
volume
scalar
a linear compbination:   COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=u_vol    COEFFICIENTS the coefficients of the arguments in your function=1.953125000000 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Number 1.953125000000 equals to 1000/512
# where 512 stands for system size and 1000 ensures the change of units from nm^3 to A^3.

scale_cnThe COMBINE action with label scale_cn calculates the following quantities:
 Quantity   
 Type   
 Description  
scale_cn
scalar
a linear compbination:  COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn      PARAMETERS the parameters of the arguments in your function=7.822   COEFFICIENTS the coefficients of the arguments in your function=0.12784454103809767  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
scale_volThe COMBINE action with label scale_vol calculates the following quantities:
 Quantity   
 Type   
 Description  
scale_vol
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=volume  PARAMETERS the parameters of the arguments in your function=13.089  COEFFICIENTS the coefficients of the arguments in your function=0.07640003056001222 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# 0.127... is the inverse value of 7.822, the mean coordination number in the starting phase
# 0.076... is the inverse value of 13.089, the mean volume in the starting phase (in A^3)

easyThe CUSTOM action with label easy calculates the following quantities:
 Quantity   
 Type   
 Description  
easy
scalar
an arbitrary function:      CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=scale_vol,scale_cn  FUNCthe function you wish to evaluate=((-0.8151947133609164)*x+(0.5791869985664506)*y)  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
difficultThe CUSTOM action with label difficult calculates the following quantities:
 Quantity   
 Type   
 Description  
difficult
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=scale_vol,scale_cn  FUNCthe function you wish to evaluate=((0.5791869985664506)*x+(0.8151947133609164)*y)  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Values above are coefficients obtained by diagonalisation of covariance matrix
# see Supplemental Material of Phys. Rev. Let. 127, 105701 (2021)

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
 ARGthe labels of the scalars on which the bias will act=easy,difficult
 SIGMAthe widths of the Gaussian hills=0.002,0.001
 HEIGHTthe heights of the Gaussian hills=3.0
 PACEthe frequency for hill addition=500
 GRID_MINthe lower bounds for the grid=-1,-1
 GRID_MAXthe upper bounds for the grid=1,1
 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001,0.001
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metad
 ARGthe labels of the scalars on which the bias will act=easy,difficult
 SIGMAthe widths of the Gaussian hills=0.002,0.001
 HEIGHTthe heights of the Gaussian hills=3.0
 PACEthe frequency for hill addition=500
 GRID_MINthe lower bounds for the grid=-1,-1
 GRID_MAXthe upper bounds for the grid=1,1
 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001,0.001
 FILE a file in which the list of added hills is stored=HILLS
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=10

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details