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
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