Project ID: plumID:21.002
Source: Crystallization/IceIh/288molecules/350K/plumed.start.dat
Originally used with PLUMED version: 2.8
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
#SETTINGS NREPLICAS=2
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for 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=1-864:3 SIGMA the width to use for the gaussian kernels=0.05 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=env1h.pdb REFERENCE_2PDB files with relative distances from central atom=env2h.pdb REFERENCE_3PDB files with relative distances from central atom=env3h.pdb REFERENCE_4PDB files with relative distances from central atom=env4h.pdb MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12} MEAN calculate the mean of all the quantities ... ENVIRONMENTSIMILARITY
# Construct a bias potential
energy: ENERGYCalculate the total potential energy of the simulation box. More details
# Construct a bias potential using VES # # Basis functions
bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=40 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=288.0 # Target distribution
td_uni: TD_UNIFORMUniform target distribution (static). More details
# 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=350.0 GRID_BINSthe number of bins used for the grid=300 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uni 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_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. 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 STEPSIZEthe step size used for the optimization=1 FES_OUTPUThow often the FES(s) should be written out to file=500 BIAS_OUTPUThow often the bias(es) should be written out to file=500 COEFFS_OUTPUT how often the coefficients should be written to file=100 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGD
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=1-864:3 SIGMA the width to use for the gaussian kernels=0.05 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=env1c.pdb REFERENCE_2PDB files with relative distances from central atom=env2c.pdb MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12} 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-0.2075)/(0.5821-0.2075)-(y-0.2319)/(0.8137-0.2319)) 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=0.05 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=1-864:3 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-0.0402)/(0.4404-0.0402)-(y-0.2319)/(0.8137-0.2319)) 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=diff2 ATthe positions of the wall=0.05 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=uwall2
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