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
tested onv2.10
tested onmaster
tested on master
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

LOADLoads 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
DISTANCECalculate 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
DISTANCECalculate 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
DISTANCECalculate 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
DISTANCECalculate 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
DISTANCECalculate 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

COMBINECalculate 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
UPPER_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
METADUsed 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
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 REWEIGHT_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 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,ghlda LABELa label for the action so that its output can be referenced in the input to other actions=hhldag
CONVERT_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 CONVERT_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
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)=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