PLUMED-NEST

Project ID: plumID:21.020
Source: hbr/ves/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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs

The UNITS action with label  calculates somethingd1: 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
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: 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
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: 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
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: 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
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: 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
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: 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

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsuwall: 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

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialcv: 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

The COMBINE action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.value
a linear compbinationBF_CHEBYSHEVChebyshev polynomial basis functions. More details         MINIMUMThe minimum of the interval on which the basis functions are defined=-3.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=2.0 ORDERThe order of the basis function expansion=48 LABELa label for the action so that its output can be referenced in the input to other actions=bf
The BF_CHEBYSHEV action with label bf calculates somethingTD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details      BIASFACTORThe bias factor used for the well-tempered distribution=50 LABELa label for the action so that its output can be referenced in the input to other actions=td
The TD_WELLTEMPERED action with label td calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ARGthe labels of the scalars on which the bias will act=cv BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf TARGET_DISTRIBUTIONthe label of the target distribution to be used=td TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300 GRID_BINSthe number of bins used for the grid=500 LABELa label for the action so that its output can be referenced in the input to other actions=b1
The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.force2
the instantaneous value of the squared force due to this bias potentialOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. 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=200 STEPSIZEthe step size used for the optimization=5.0 TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=10 FES_OUTPUThow often the FES(s) should be written out to file=1000 LABELa label for the action so that its output can be referenced in the input to other actions=opt

The OPT_AVERAGED_SGD action with label opt calculates the following quantities:
 Quantity   
 Description  
opt.value
a scalarREWEIGHT_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=b1.bias TEMPthe system temperature=300 LABELa label for the action so that its output can be referenced in the input to other actions=bias

The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasHISTOGRAMAccumulate 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
  LABELa label for the action so that its output can be referenced in the input to other actions=hh
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.value
the estimate of the histogram as a function of the argument that was obtainedCONVERT_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

The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
the free energy surfaceDUMPGRIDOutput 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