Project ID: plumID:21.020
Source: hbr/metad/plumed.inp
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
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UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1 NOPBC ignore the periodic boundary conditions when calculating distances d3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 NOPBC ignore the periodic boundary conditions when calculating distances d4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2 NOPBC ignore the periodic boundary conditions when calculating distances d5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 NOPBC ignore the periodic boundary conditions when calculating distances d6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 NOPBC ignore the periodic boundary conditions when calculating distances
uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5,d6 ATthe positions of the wall=3.0,3.0,3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=100,100,100,100,100,100 cv: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6 COEFFICIENTS the coefficients of the arguments in your function=0.661,-0.656,-0.328,0.011,-0.021,0.157 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cv PACEthe frequency for hill addition=200 HEIGHTthe heights of the Gaussian hills=5.0 SIGMAthe widths of the Gaussian hills=0.2 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=50 GRID_MINthe lower bounds for the grid=-3.0 GRID_MAXthe upper bounds for the grid=2.0 GRID_BINthe number of bins for the grid=5000 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=10 LABELa label for the action so that its output can be referenced in the input to other actions=b1
CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=100.0 LABELa label for the action so that its output can be referenced in the input to other actions=cnst BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=cnst LABELa label for the action so that its output can be referenced in the input to other actions=dummy
REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=300 LABELa label for the action so that its output can be referenced in the input to other actions=bias REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details ARG the biases that must be taken into account when reweighting=dummy.bias TEMPthe system temperature=300 LABELa label for the action so that its output can be referenced in the input to other actions=dum
HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ... ARGthe quantities that are being used to construct the histogram=cv GRID_MIN the lower bounds for the grid=-2.0 GRID_MAX the upper bounds for the grid=2.0 GRID_BINthe number of bins for the grid=4000 BANDWIDTHthe bandwidths for kernel density esimtation=0.02 CLEAR the frequency with whihc to clear the data that is being averaged=200000 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,dum LABELa label for the action so that its output can be referenced in the input to other actions=hh ... HISTOGRAM
CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hh TEMPthe temperature at which you are operating=300.0 LABELa label for the action so that its output can be referenced in the input to other actions=ff
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ff FILE the file on which to write the grid=fes STRIDE the frequency with which the grid should be output to the file=200000 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=2000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,cv,b1.bias STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar