PLUMED-NEST-TEST-SITE

Project ID: plumID:21.013
Source: ch4-diss/ni001/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 somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../data/ReweightGeomFES.cpp

DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=66-69 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=65    MAXcalculate the maximum value={BETA=0.010} LABELa label for the action so that its output can be referenced in the input to other actions=d1
The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.max
the maximum colvar
d1.value
the DISTANCES between the each pair of atoms that were specifiedDISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=65    GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-64  MINcalculate the minimum value={BETA=100.0} LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=2.5} LABELa label for the action so that its output can be referenced in the input to other actions=metalc
The DISTANCES action with label metalc calculates the following quantities:
 Quantity   
 Description  
metalc.lessthan
the number of colvars that have a value less than a threshold
metalc.min
the minimum colvar
metalc.value
the DISTANCES between the each pair of atoms that were specifiedDISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=66-69 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-64  MINcalculate the minimum value={BETA=100.0} LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=2.0} LABELa label for the action so that its output can be referenced in the input to other actions=metalh
The DISTANCES action with label metalh calculates the following quantities:
 Quantity   
 Description  
metalh.lessthan
the number of colvars that have a value less than a threshold
metalh.min
the minimum colvar
metalh.value
the DISTANCES between the each pair of atoms that were specifiedANGLESCalculate functions of the distribution of angles. More details    GROUPAA group of central atoms about which angles should be calculated=65    GROUPBWhen used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPB=66-69 BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0.5pi UPPER=0.7pi} SWITCHthe switching function specifies that only those bonds that have a length that is less than a certain threshold are considered={RATIONAL D_0=1.50 R_0=0.25} LABELa label for the action so that its output can be referenced in the input to other actions=ang
The ANGLES action with label ang calculates the following quantities:
 Quantity   
 Description  
ang.value
the ANGLE for each set of three atoms that were specified
ang.between
the number of colvars that have a value that lies in a particular intervalCOORDINATIONNUMBERCalculate 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=65    SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=66-69 R_0The r_0 parameter of the switching function=1.75 NN The n parameter of the switching function =12        MEAN calculate the mean of all the quantities             LABELa label for the action so that its output can be referenced in the input to other actions=d3

The COORDINATIONNUMBER action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.mean
the mean of the colvars
d3.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=d1.max,metalc.lessthan,metalh.lessthan,ang.between COEFFICIENTS the coefficients of the arguments in your function=0.812,0.283,-0.103,-0.501 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 compbinationUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=metalc.min,cv ATthe positions of the wall=4.00,5.0 KAPPAthe force constant for the wall=100,1 LABELa label for the action so that its output can be referenced in the input to other actions=wall1
The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Description  
wall1.bias
the instantaneous value of the bias potential
wall1.force2
the instantaneous value of the squared force due to this bias potentialUWALLSAdd lower walls to a vector of quantities More details      DATAthe values you want to restrain=d1           ATthe radius of the sphere=1.80     KAPPAthe force constant for the wall=500   LABELa label for the action so that its output can be referenced in the input to other actions=wall2
The UWALLS action with label wall2 calculates the following quantities:
 Quantity   
 Description  
wall2.bias
the instantaneous value of the bias potential
wall2.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=d3.mean       ATthe positions of the wall=2.95     KAPPAthe force constant for the wall=1000  LABELa label for the action so that its output can be referenced in the input to other actions=wall3

The LOWER_WALLS action with label wall3 calculates the following quantities:
 Quantity   
 Description  
wall3.bias
the instantaneous value of the bias potential
wall3.force2
the instantaneous value of the squared force due to this bias potentialMETADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=cv
  SIGMAthe widths of the Gaussian hills=0.05
  HEIGHTthe heights of the Gaussian hills=0.25
  PACEthe frequency for hill addition=1000
  BIASFACTORuse well tempered metadynamics and use this bias factor=25
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=500
  GRID_MINthe lower bounds for the grid=-3.0
  GRID_MAXthe upper bounds for the grid=3.0
  GRID_BINthe number of bins for the grid=1200
  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=1
  LABELa label for the action so that its output can be referenced in the input to other actions=b1
... METAD

The METAD action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
b1.rct
the reweighting factor c(t)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=500 LABELa label for the action so that its output can be referenced in the input to other actions=bias
The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics biasREWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=500 ARG=cv              LABEL=gcv
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=500 ARG=d1.max          LABEL=g1
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=500 ARG=metalc.lessthan LABEL=g2
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=500 ARG=ang.between     LABEL=g3
REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details    TEMPthe system temperature=500 ARG the biases that must be taken into account when reweighting=wall1.bias,wall2.bias LABELa label for the action so that its output can be referenced in the input to other actions=wbias

The REWEIGHT_BIAS action with label wbias calculates the following quantities:
 Quantity   
 Description  
wbias.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=-3.0
  GRID_MAX the upper bounds for the grid=3.0
  GRID_BINthe number of bins for the grid=6000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,wbias
  CLEAR the frequency with whihc to clear the data that is being averaged=5000000
  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 obtainedHISTOGRAMAccumulate 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=-3.0
  GRID_MAX the upper bounds for the grid=3.0
  GRID_BINthe number of bins for the grid=6000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,wbias,gcv
  CLEAR the frequency with whihc to clear the data that is being averaged=5000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hhg
... HISTOGRAM

The HISTOGRAM action with label hhg calculates the following quantities:
 Quantity   
 Description  
hhg.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=d1.max
  GRID_MIN the lower bounds for the grid=1.0
  GRID_MAX the upper bounds for the grid=3.5
  GRID_BINthe number of bins for the grid=2500
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,wbias,g1
  CLEAR the frequency with whihc to clear the data that is being averaged=5000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hh1
... HISTOGRAM

The HISTOGRAM action with label hh1 calculates the following quantities:
 Quantity   
 Description  
hh1.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=metalc.lessthan
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=5.0
  GRID_BINthe number of bins for the grid=2500
  BANDWIDTHthe bandwidths for kernel density esimtation=0.02
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,wbias,g2
  CLEAR the frequency with whihc to clear the data that is being averaged=5000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hh2
... HISTOGRAM

The HISTOGRAM action with label hh2 calculates the following quantities:
 Quantity   
 Description  
hh2.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=ang.between
  GRID_MIN the lower bounds for the grid=1.5
  GRID_MAX the upper bounds for the grid=4.5
  GRID_BINthe number of bins for the grid=1500
  BANDWIDTHthe bandwidths for kernel density esimtation=0.02
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,wbias,g3
  CLEAR the frequency with whihc to clear the data that is being averaged=5000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hh3
... HISTOGRAM

The HISTOGRAM action with label hh3 calculates the following quantities:
 Quantity   
 Description  
hh3.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=500.0 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 surfaceCONVERT_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)=hhg TEMPthe temperature at which you are operating=500.0 LABELa label for the action so that its output can be referenced in the input to other actions=ffg
The CONVERT_TO_FES action with label ffg calculates the following quantities:
 Quantity   
 Description  
ffg.value
the free energy surfaceCONVERT_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)=hh1 TEMPthe temperature at which you are operating=500.0 LABELa label for the action so that its output can be referenced in the input to other actions=ff1
The CONVERT_TO_FES action with label ff1 calculates the following quantities:
 Quantity   
 Description  
ff1.value
the free energy surfaceCONVERT_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)=hh2 TEMPthe temperature at which you are operating=500.0 LABELa label for the action so that its output can be referenced in the input to other actions=ff2
The CONVERT_TO_FES action with label ff2 calculates the following quantities:
 Quantity   
 Description  
ff2.value
the free energy surfaceCONVERT_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)=hh3 TEMPthe temperature at which you are operating=500.0 LABELa label for the action so that its output can be referenced in the input to other actions=ff3

The CONVERT_TO_FES action with label ff3 calculates the following quantities:
 Quantity   
 Description  
ff3.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=1000000
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)=ffg FILE the file on which to write the grid=fesg STRIDE the frequency with which the grid should be output to the file=1000000
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)=ff1 FILE the file on which to write the grid=fes1 STRIDE the frequency with which the grid should be output to the file=1000000
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)=ff2 FILE the file on which to write the grid=fes2 STRIDE the frequency with which the grid should be output to the file=1000000
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)=ff3 FILE the file on which to write the grid=fes3 STRIDE the frequency with which the grid should be output to the file=1000000

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=d1.max,metalc.lessthan,metalh.lessthan,ang.between,d3.mean,cv,b1.bias,b1.rct 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