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
tested onv2.10
tested onmaster
#spib_learned_cv
#
#RESTART
  
q6: Q6Calculate sixth order Steinhardt parameters. This action is a shortcut. More details SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESAthis keyword is used for colvars such as the coordination number=1-256 SPECIESBthis 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

q4: Q4Calculate fourth order Steinhardt parameters. This action is a shortcut. More details SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESAthis keyword is used for colvars such as the coordination number=1-256 SPECIESBthis 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


ene: ENERGYCalculate the total potential energy of the simulation box. More details
vol: VOLUMECalculate the volume of the simulation box. More details


COMBINECalculate 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

COMBINECalculate 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


COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details ...
SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.33 D_MAX=0.6}
SPECIESAthis keyword is used for colvars such as the coordination number=1-256 SPECIESBthis keyword is used for colvars such as the coordination number=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={RATIONAL R_0=4.0 D_MAX=5.0}
MORE_THAN2calculate the number of variables that are more than a certain target value={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

cv1_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

cv2_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

cv1: 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 

cv2: 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 

metad: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. 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]
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