Project ID: plumID:23.046
Source: github/MccJ25/plumed.dat
Originally used with PLUMED version: 2.7.1
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
# This is the plumed file to use on linear native MJ25 - using 2 CVs
#RESTART 

# units UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A # Molecule WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-292 # distances # first is 1N-8CD and the others are for the CA of resid19 to resids 1to8 DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,246 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=12,246 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=19,246 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=29,246 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=36,246 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=53,246 LABELa label for the action so that its output can be referenced in the input to other actions=d6 DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=77,246 LABELa label for the action so that its output can be referenced in the input to other actions=d7 DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=83,246 LABELa label for the action so that its output can be referenced in the input to other actions=d8
CV1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,91 CV2: COMBINECalculate a polynomial combination of a set of other variables. More details ... ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8 COEFFICIENTS the coefficients of the arguments in your function=-0.3221,-0.0361,-0.1063,-0.1538,-0.0913,-0.5176,-0.6589,-0.3867 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ...
# activade well-tempered metadynamics metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=CV1,CV2 ... # Deposit a Gaussian every 500 time steps (= 1ps), with initial height # equal to 5 kJ/mol and bias factor equal to 80 # This version we use a double value for the height and bias factor PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=5 BIASFACTORuse well tempered metadynamics and use this bias factor=80 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 # Gaussian width (sigma) should be chosen based on the CV fluctuations in unbiased run # try 1/2 or 1/3 of the estimated fluctuations # standard deviation for distance 1N - 8N was 0.91 # standard deviation for CA distances was between 6.84-7.06 SIGMAthe widths of the Gaussian hills=0.5,3.5 # Gaussians will be written to file and also stored on grid FILE a file in which the list of added hills is stored=HILLS GRID_WSTRIDEwrite the grid to a file every N steps=100000 #GRID_RFILE=grid1.dat GRID_WFILEthe file on which to write the grid=grid1.dat GRID_NOSPLINE don't use spline interpolation with grids GRID_MINthe lower bounds for the grid=0,-200 GRID_MAXthe upper bounds for the grid=35,0 GRID_BINthe number of bins for the grid=350,500 ... # Print both collective variables on COLVAR file every 100 steps PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,CV1,CV2,metad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100