PLUMED-NEST

Project ID: plumID:20.018
Source: na/plumed.inp
Originally used with PLUMED version: 2.6-mod
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=96.485

The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../src/bias/ReweightGeomFES.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairEntropy.cpp

ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=ene
The ENERGY action with label ene calculates somethingVOLUMECalculate the volume the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=vol

The VOLUME action with label vol calculates the following quantities:
 Quantity   
 Description  
vol.value
the volume of simulation boxCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ene,vol COEFFICIENTS the coefficients of the arguments in your function=1.0,1.0/1602176.5 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=enthalpy
The COMBINE action with label enthalpy calculates the following quantities:
 Quantity   
 Description  
enthalpy.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=enthalpy COEFFICIENTS the coefficients of the arguments in your function=1.0/250 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=sh

The COMBINE action with label sh calculates the following quantities:
 Quantity   
 Description  
sh.value
a linear compbinationCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-250 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 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=cn
The COORDINATIONNUMBER action with label cn calculates the following quantities:
 Quantity   
 Description  
cn.moment
the moments of the distribution
cn.value
the coordination numbers of the specified atomsQ6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-250 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 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=q6
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.mean
the mean of the colvars
q6.value
the norms of the vectors of spherical harmonic coefficientsLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=q6 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0} 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=q6l

The LOCAL_AVERAGE action with label q6l calculates the following quantities:
 Quantity   
 Description  
q6l.mean
the mean of the colvars
q6l.value
the values of the local averagesLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=q6l.mean ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=dummy

The LOWER_WALLS action with label dummy calculates the following quantities:
 Quantity   
 Description  
dummy.bias
the instantaneous value of the bias potential
dummy.force2
the instantaneous value of the squared force due to this bias potentialPAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ...
  ATOMSthe atoms that are being used to calculate the RDF=1-250
  MAXRthe maximum distance to use for the rdf=6.5
  SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.125
  NHIST=130
  LABELa label for the action so that its output can be referenced in the input to other actions=ss
... PAIRENTROPY

The PAIRENTROPY action with label ss calculates the following quantities:
 Quantity   
 Description  
ss.value
the KL-entropy that is computed from the radial distribution functionMETADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=sh,ss
  SIGMAthe widths of the Gaussian hills=0.002,0.10
  HEIGHTthe heights of the Gaussian hills=0.025
  PACEthe frequency for hill addition=2500
  BIASFACTORuse well tempered metadynamics and use this bias factor=30
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=375
  GRID_MINthe lower bounds for the grid=-1.10,-6.0
  GRID_MAXthe upper bounds for the grid=-0.95,-1.0
  GRID_BINthe number of bins for the grid=750,500
  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=375 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 ARG=ss       TEMP=375 LABEL=gss
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=q6l.mean TEMP=375 LABEL=gq6l

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=ss GRID_MIN the lower bounds for the grid=-6.0 GRID_MAX the upper bounds for the grid=-1.0 GRID_BINthe number of bins for the grid=1000 BANDWIDTHthe bandwidths for kernel density esimtation=0.02 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=hss
The HISTOGRAM action with label hss calculates the following quantities:
 Quantity   
 Description  
hss.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=q6l.mean GRID_MIN the lower bounds for the grid=0.05 GRID_MAX the upper bounds for the grid=0.5 GRID_BINthe number of bins for the grid=900 BANDWIDTHthe bandwidths for kernel density esimtation=0.004 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=hq6l
The HISTOGRAM action with label hq6l calculates the following quantities:
 Quantity   
 Description  
hq6l.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=ss GRID_MIN the lower bounds for the grid=-6.0 GRID_MAX the upper bounds for the grid=-1.0 GRID_BINthe number of bins for the grid=1000 BANDWIDTHthe bandwidths for kernel density esimtation=0.02 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gss LABELa label for the action so that its output can be referenced in the input to other actions=hssg
The HISTOGRAM action with label hssg calculates the following quantities:
 Quantity   
 Description  
hssg.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=q6l.mean GRID_MIN the lower bounds for the grid=0.05 GRID_MAX the upper bounds for the grid=0.5 GRID_BINthe number of bins for the grid=900 BANDWIDTHthe bandwidths for kernel density esimtation=0.004 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gq6l LABELa label for the action so that its output can be referenced in the input to other actions=hq6lg

The HISTOGRAM action with label hq6lg calculates the following quantities:
 Quantity   
 Description  
hq6lg.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)=hss   TEMPthe temperature at which you are operating=375 LABELa label for the action so that its output can be referenced in the input to other actions=fss
The CONVERT_TO_FES action with label fss calculates the following quantities:
 Quantity   
 Description  
fss.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)=hq6l  TEMPthe temperature at which you are operating=375 LABELa label for the action so that its output can be referenced in the input to other actions=fq6l
The CONVERT_TO_FES action with label fq6l calculates the following quantities:
 Quantity   
 Description  
fq6l.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)=hssg  TEMPthe temperature at which you are operating=375 LABELa label for the action so that its output can be referenced in the input to other actions=fssg
The CONVERT_TO_FES action with label fssg calculates the following quantities:
 Quantity   
 Description  
fssg.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)=hq6lg TEMPthe temperature at which you are operating=375 LABELa label for the action so that its output can be referenced in the input to other actions=fq6lg

The CONVERT_TO_FES action with label fq6lg calculates the following quantities:
 Quantity   
 Description  
fq6lg.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)=fss   FILE the file on which to write the grid=fesss   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)=fq6l  FILE the file on which to write the grid=fesq6l  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)=fssg  FILE the file on which to write the grid=fesssg  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)=fq6lg FILE the file on which to write the grid=fesq6lg 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=50000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sh,ss,q6l.mean,b1.bias,b1.rct 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