PLUMED-NEST

Project ID: plumID:19.080
Source: ohco2/symm-sample/plumed.inp
Originally used with PLUMED version: 2.4.1
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 somethingCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d1
The COORDINATION action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d2

The COORDINATION action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the value of the coordinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 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=1.0
  GRID_BINthe number of bins for the grid=500
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01
  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 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)=hh FILE the file on which to write the grid=histo STRIDE the frequency with which the grid should be output to the file=40000
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=40000

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=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nm 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