**Project ID:** plumID:19.050

**Source:** plumed_reweight.dat

**Originally used with PLUMED version:** not specified

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

# The consequence of including this command is that the bias values that are calculated # by the METAD action are values for the final simulation bias.RESTART# These two commands recompute the CV that was biased in the metadynamics calculation.Activate restart. More detailscont:DISTANCE_FROM_CONTOUR...Calculate the perpendicular distance from a Willard-Chandler dividing surface. More detailsPOSITIONS=2-2400:12,10-2400:12the positions of the atoms that we are calculating the contour fromATOM=2413The atom whose perpendicular distance we are calculating from the contourBANDWIDTH=3.0,3.0,3.0the bandwidths for kernel density esimtationDIR=zthe direction perpendicular to the contour that you are looking forCONTOUR=0.42 ... # This command is used to calculate the final metadynamics bias. This quantity is # required because it used when reweighting each of the trajectory frames.the value we would like for the contourmm:METAD...Used to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionscont.qdistSIGMA=0.5the widths of the Gaussian hillsHEIGHT=1.3the heights of the Gaussian hillsBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=325the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=2000000000 # This is large so Gaussians are not added and the bias is constant.the frequency for hill additionGRID_MIN=-15.0the lower bounds for the gridGRID_MAX=100.0the upper bounds for the gridGRID_BIN=115000the number of bins for the gridADAPTIVE=GEOMuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.05the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=6.00 ...the upper bounds for the sigmas (in CV units) when using adaptive hillsuwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingcont.qdistAT=50.0the positions of the wallKAPPA=1.0the force constant for the wallEXP=2 # The two lines below instruct PLUMED to calculate the distance between the adsorbate and # the isosurface. Notice, however, that, because we are now doing the analysis all of # the atoms in the membrane are used when we calculate the density.the powers for the wallscont2:DISTANCE_FROM_CONTOUR...Calculate the perpendicular distance from a Willard-Chandler dividing surface. More detailsPOSITIONS=1-2400the positions of the atoms that we are calculating the contour fromATOM=2413The atom whose perpendicular distance we are calculating from the contourBANDWIDTH=0.6,0.6,0.6the bandwidths for kernel density esimtationDIR=zthe direction perpendicular to the contour that you are looking forCONTOUR=7.29 ... # When reweighting we must take both the MEAD and UPPER_WALLS into accountthe value we would like for the contourbias:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=*.biasthe input to this functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionscont2.*,biasFILE=COLVAR-reweightthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output