PLUMED-NEST

Project ID: plumID:19.080
Source: h3/explicit/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 somethingDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 LABELa label for the action so that its output can be referenced in the input to other actions=d1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,3 LABELa label for the action so that its output can be referenced in the input to other actions=d2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 LABELa label for the action so that its output can be referenced in the input to other actions=d3

The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsCOMBINECalculate 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=1.0,-1.0 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=cv
The COMBINE action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d3 COEFFICIENTS the coefficients of the arguments in your function=-1.0,1.0 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=block1
The COMBINE action with label block1 calculates the following quantities:
 Quantity   
 Description  
block1.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d2,d3 COEFFICIENTS the coefficients of the arguments in your function=-1.0,1.0 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=block2

The COMBINE action with label block2 calculates the following quantities:
 Quantity   
 Description  
block2.value
a linear compbinationUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2 ATthe positions of the wall=2.5,2.5 KAPPAthe force constant for the wall=100.0,100.0 LABELa label for the action so that its output can be referenced in the input to other actions=constrain
The UPPER_WALLS action with label constrain calculates the following quantities:
 Quantity   
 Description  
constrain.bias
the instantaneous value of the bias potential
constrain.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=block1,block2 ATthe positions of the wall=0.0,0.0 KAPPAthe force constant for the wall=1000.0,1000.0 LABELa label for the action so that its output can be referenced in the input to other actions=cone

The LOWER_WALLS action with label cone calculates the following quantities:
 Quantity   
 Description  
cone.bias
the instantaneous value of the bias potential
cone.force2
the instantaneous value of the squared force due to this bias potentialHISTOGRAMAccumulate 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=-2.5
  GRID_MAX the upper bounds for the grid=2.5
  GRID_BINthe number of bins for the grid=1000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.02
  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=10000000
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=10000000


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=10000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,cv STRIDE the frequency with which the quantities of interest should be output=10000 FILEthe name of the file on which to output these quantities=colvar