PLUMED-NEST

Project ID: plumID:20.018
Source: da-tt/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=kcal/mol

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

DISTANCECalculate the distance between a pair 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 between a pair 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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4 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 atomsDISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,5 LABELa label for the action so that its output can be referenced in the input to other actions=d4
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6 LABEla label for the action so that its output can be referenced in the input to other actions=d5
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,6 LABELa label for the action so that its output can be referenced in the input to other actions=d6

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.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,d3,d4,d6 COEFFICIENTS the coefficients of the arguments in your function=-0.05,0.21,-0.08,0.69,0.69 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=hlda

The COMBINE action with label hlda calculates the following quantities:
 Quantity   
 Description  
hlda.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=d4,d6 ATthe positions of the wall=5.0,5.0 KAPPAthe force constant for the wall=50,50 LABELa label for the action so that its output can be referenced in the input to other actions=walls

The UPPER_WALLS action with label walls calculates the following quantities:
 Quantity   
 Description  
walls.bias
the instantaneous value of the bias potential
walls.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=hlda
  SIGMAthe widths of the Gaussian hills=0.15
  HEIGHTthe heights of the Gaussian hills=1.0
  PACEthe frequency for hill addition=100
  TTBIASFACTORuse transition tempered metadynamics with this bias factor=25
  CALC_TRANSITION_BIAS Set to TRUE if you want to compute a metadynamics transition bias V*(t)
  TRANSITIONWELL0This keyword appears multiple times as TRANSITIONWELL followed by an integer=2.0
  TRANSITIONWELL1This keyword appears multiple times as TRANSITIONWELL followed by an integer=5.0
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=600
  GRID_MINthe lower bounds for the grid=1.0
  GRID_MAXthe upper bounds for the grid=9.0
  GRID_BINthe number of bins for the grid=1600
  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)
b1.transbias
the metadynamics transition bias V*(t)REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details ARG the biases that must be taken into account when reweighting=b1.bias    TEMPthe system temperature=600 LABELa label for the action so that its output can be referenced in the input to other actions=bias
The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasREWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=hlda    TEMP=600 LABEL=ghlda

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=hlda       GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=9.0         GRID_BINthe number of bins for the grid=4000    BANDWIDTHthe bandwidths for kernel density esimtation=0.01      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=hhlda
The HISTOGRAM action with label hhlda calculates the following quantities:
 Quantity   
 Description  
hhlda.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=hlda       GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=9.0         GRID_BINthe number of bins for the grid=4000    BANDWIDTHthe bandwidths for kernel density esimtation=0.01      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,ghlda   LABELa label for the action so that its output can be referenced in the input to other actions=hhldag

The HISTOGRAM action with label hhldag calculates the following quantities:
 Quantity   
 Description  
hhldag.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)=hhlda     TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fhlda
The CONVERT_TO_FES action with label fhlda calculates the following quantities:
 Quantity   
 Description  
fhlda.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)=hhldag     TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fhldag

The CONVERT_TO_FES action with label fhldag calculates the following quantities:
 Quantity   
 Description  
fhldag.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)=fhlda   FILE the file on which to write the grid=feshlda   STRIDE the frequency with which the grid should be output to the file=500000
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)=fhldag   FILE the file on which to write the grid=feshldag   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=2000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d4,d6,hlda,b1.bias,b1.rct 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