PLUMED-NEST-TEST-SITE

Project ID: plumID:21.013
Source: ch4-base/asymm-sample/plumed.inp
Originally used with PLUMED version: 2.6
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 ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=2-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 MEAN calculate the mean of all the quantities MOMENTSthe list of moments that you would like to calculate=2 LABELa label for the action so that its output can be referenced in the input to other actions=nm2
The COORDINATIONNUMBER action with label nm2 calculates the following quantities:
 Quantity   
 Description  
nm2.mean
the mean of the colvars
nm2.moment
the moments of the distribution
nm2.value
the coordination numbers of the specified atomsCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=nm2.moment-2 POWERS the powers to which you are raising each of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=nm

The COMBINE action with label nm calculates the following quantities:
 Quantity   
 Description  
nm.value
a linear compbinationHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=nm
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=0.5
  GRID_BINthe number of bins for the grid=5000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.005
  LABELa label for the action so that its output can be referenced in the input to other actions=targetdist
... HISTOGRAM

The HISTOGRAM action with label targetdist calculates the following quantities:
 Quantity   
 Description  
targetdist.value
the estimate of the histogram as a function of the argument that was obtainedDUMPGRIDOutput 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)=targetdist FILE the file on which to write the grid=histo STRIDE the frequency with which the grid should be output to the file=500000

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=100000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nm2.moment-2,nm STRIDE the frequency with which the quantities of interest should be output=50000 FILEthe name of the file on which to output these quantities=colvar