PLUMED-NEST

Project ID: plumID:23.036
Source: melt/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: Q6Calculate sixth order Steinhardt parameters. More details SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=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 the following quantities:
 Quantity   
 Description  
q6.mean
the mean of the colvars
q6.value
the norms of the vectors of spherical harmonic coefficientsq4: Q4Calculate fourth order Steinhardt parameters. More details SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=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 the following quantities:
 Quantity   
 Description  
q4.mean
the mean of the colvars
q4.value
the norms of the vectors of spherical harmonic coefficientsene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingvol: VOLUMECalculate the volume the simulation box. More details


The VOLUME action with label vol calculates the volume of simulation boxCOMBINECalculate a polynomial combination of a set of other variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=enthalpy
 ARGthe values input to this function=ene,vol
 COEFFICIENTS the coefficients of the arguments in your function=1.0,0.060221409
 PERIODICif 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 the following quantities:
 Quantity   
 Description  
enthalpy.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=h
 ARGthe values 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
 PERIODICif 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 the following quantities:
 Quantity   
 Description  
h.value
a linear compbinationCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details ...
SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.33 D_MAX=0.6}
SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512
MEAN calculate the mean of all the quantities
MOMENTSthe list of moments that you would like to calculate=2
MORE_THAN1calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=4.0 D_MAX=5.0}
MORE_THAN2calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0 D_MAX=6.0}
LABELa 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 the following quantities:
 Quantity   
 Description  
cn.mean
the mean of the colvars
cn.moment
the moments of the distribution
cn.value
the coordination numbers of the specified atomscv1_l: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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=8.77874,-11.6973,0.157351,0.0816257,0.00418239,-0.0177146,-0.0163215 PERIODICif 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 the following quantities:
 Quantity   
 Description  
cv1_l.value
a linear compbinationcv2_l: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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=20.4484,12.8081,-1.74684,0.763133,-0.00471387,0.0117218,0.000533273 PERIODICif 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 the following quantities:
 Quantity   
 Description  
cv2_l.value
a linear compbinationcv1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cv1_l FUNCthe function you wish to evaluate=x-28.139110 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 

The MATHEVAL action with label cv1 calculates the following quantities:
 Quantity   
 Description  
cv1.value
an arbitrary functioncv2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cv2_l FUNCthe function you wish to evaluate=x-8.283814 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 

The MATHEVAL action with label cv2 calculates the following quantities:
 Quantity   
 Description  
cv2.value
an arbitrary functionmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cv1,cv2 SIGMAthe widths of the Gaussian hills=0.15,0.15 HEIGHTthe heights of the Gaussian hills=5 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1125 GRID_MINthe lower bounds for the grid=-6,-7 GRID_MAXthe upper bounds for the grid=4,7 GRID_BINthe number of bins for the grid=150,175 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)PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv1,cv2,q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h,metad.bias,metad.rbias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100