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
Click on the labels of the actions for more information on what each action computes
# 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. RESTARTActivate restart. More details # These two commands recompute the CV that was biased in the metadynamics calculation. cont: DISTANCE_FROM_CONTOURCalculate the perpendicular distance from a Willard-Chandler dividing surface. More details ... POSITIONSthe positions of the atoms that we are calculating the contour from=2-2400:12,10-2400:12 ATOMThe atom whose perpendicular distance we are calculating from the contour=2413 BANDWIDTHthe bandwidths for kernel density esimtation=3.0,3.0,3.0 DIRthe direction perpendicular to the contour that you are looking for=z CONTOURthe value we would like for the contour=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. mm: METADUsed to performed metadynamics on one or more collective variables. More details ... ARGthe labels of the scalars on which the bias will act=cont.qdist SIGMAthe widths of the Gaussian hills=0.5 HEIGHTthe heights of the Gaussian hills=1.3 BIASFACTORuse well tempered metadynamics and use this bias factor=25 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=325 PACEthe frequency for hill addition=2000000000 # This is large so Gaussians are not added and the bias is constant. GRID_MINthe lower bounds for the grid=-15.0 GRID_MAXthe upper bounds for the grid=100.0 GRID_BINthe number of bins for the grid=115000 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.05 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=6.00 ... uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cont.qdist ATthe positions of the wall=50.0 KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=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. cont2: DISTANCE_FROM_CONTOURCalculate the perpendicular distance from a Willard-Chandler dividing surface. More details ... POSITIONSthe positions of the atoms that we are calculating the contour from=1-2400 ATOMThe atom whose perpendicular distance we are calculating from the contour=2413 BANDWIDTHthe bandwidths for kernel density esimtation=0.6,0.6,0.6 DIRthe direction perpendicular to the contour that you are looking for=z CONTOURthe value we would like for the contour=7.29 ... # When reweighting we must take both the MEAD and UPPER_WALLS into account bias: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=*.bias PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cont2.*,bias FILEthe name of the file on which to output these quantities=COLVAR-reweight STRIDE the frequency with which the quantities of interest should be output=1