Project ID: plumID:20.010
Source: BiasedSimulations/96molecules/280K/plumed.dat
Originally used with PLUMED version: 2.6-dev
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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

RESTARTActivate restart. More details
vol: VOLUMECalculate the volume of the simulation box. More details
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details ... SPECIESthis keyword is used for colvars such as coordination number=1-288:3 SIGMA the width to use for the gaussian kernels=0.055 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM LABELa label for the action so that its output can be referenced in the input to other actions=refcv REFERENCE_1PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env1.pdb REFERENCE_2PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env2.pdb REFERENCE_3PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env3.pdb REFERENCE_4PDB files with relative distances from central atom=../../../Environments/IceIhExtendedEnvironments/env4.pdb MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=12 MM=24} MEAN calculate the mean of all the quantities ... ENVIRONMENTSIMILARITY
# Construct a bias potential using VES # # Basis functions
bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=20 MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=96.0 # Target distribution
td_welltemp: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=50 # Expansion
VES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ... ARGthe labels of the scalars on which the bias will act=refcv.morethan BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=280.0 GRID_BINSthe number of bins used for the grid=300 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_welltemp LABELa label for the action so that its output can be referenced in the input to other actions=b1 ... VES_LINEAR_EXPANSION
# Optimization algorithm
OPT_DUMMYDummy optimizer for debugging. This action has hidden defaults. More details ... BIASthe label of the VES bias to be optimized=b1 STRIDEthe frequency of updating the coefficients given in the number of MD steps=500 LABELa label for the action so that its output can be referenced in the input to other actions=o1 #MULTIPLE_WALKERS COEFFS_OUTPUT how often the coefficients should be written to file=100 ... OPT_DUMMY
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details ... SPECIESthis keyword is used for colvars such as coordination number=1-288:3 SIGMA the width to use for the gaussian kernels=0.055 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM LABELa label for the action so that its output can be referenced in the input to other actions=refcv2 REFERENCE_1PDB files with relative distances from central atom=../../../Environments/IceIcExtendedEnvironments/env1.pdb REFERENCE_2PDB files with relative distances from central atom=../../../Environments/IceIcExtendedEnvironments/env2.pdb MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=12 MM=24} MEAN calculate the mean of all the quantities ... ENVIRONMENTSIMILARITY
diff: 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=refcv2.mean,refcv.mean FUNCthe function you wish to evaluate=((x-0.26)/(0.58-0.26)-(y-0.29)/(0.80-0.29)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.04 KAPPAthe force constant for the wall=100000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
# Avoid other structures Q6Calculate sixth order Steinhardt parameters. This action is a shortcut. More details SPECIESthis keyword is used for colvars such as coordination number=1-288:3 SWITCHthe switching function that it used in the construction of the contact matrix={CUBIC D_0=0.3 D_MAX=0.35} VMEAN calculate the norm of the mean vector LABELa label for the action so that its output can be referenced in the input to other actions=q6 diff2: 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=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=((x-0.0668781995)/(0.39184059-0.0668781995)-(y-0.2899390548628429)/(0.7838534089775562-0.2899390548628429)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 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