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
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=96.485

LOADLoads 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
VOLUMECalculate the volume of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=vol

COMBINECalculate 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 COMBINECalculate 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
COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthis keyword is used for colvars such as coordination number=1-250 SWITCHthe switching function that it used in the construction of the contact matrix={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 Q6Calculate sixth order Steinhardt parameters. More details SPECIESthis keyword is used for colvars such as coordination number=1-250 SWITCHthe switching function that it used in the construction of the contact matrix={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 LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESthis keyword is used for colvars such as coordination number=q6 SWITCHthe switching function that it used in the construction of the contact matrix={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
LOWER_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
PAIRENTROPYCalculate 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
METADUsed 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
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 REWEIGHT_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 HISTOGRAMAccumulate 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 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,gss LABELa label for the action so that its output can be referenced in the input to other actions=hssg HISTOGRAMAccumulate 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
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)=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 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)=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 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)=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 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)=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
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)=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