**Project ID:** plumID:23.046

**Source:** github/Uln/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

# This is the plumed file to use on linear native MJ25 - using 2 CVs #RESTART

# unitsUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths

# MoleculeWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-219the atoms that make up a molecule that you wish to align

# distances # first is 1N-8CD and the others are for the CA of resid19 to resids 1to8DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd1DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=12,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd2DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=32,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd3DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=51,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd4DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=58,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd5DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=82,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd6DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=89,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd7DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=111,169the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd8CV1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,116the pair of atom that we are calculating the distance betweenCV2:COMBINE...Calculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond1,d2,d3,d4,d5,d6,d7,d8COEFFICIENTS=-0.6155,-0.0608,-0.3019,-0.1527,-0.4919,-0.1703,-0.4723,-0.0949the coefficients of the arguments in your functionPERIODIC=NO ...if the output of your function is periodic then you should specify the periodicity of the function

# activade well-tempered metadynamicsmetad:METADUsed 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 actionsCV1,CV2... # Deposit a Gaussian every 500 time steps (= 1ps), with initial height # equal to 2.5 kJ/mol and bias factor equal to 40 # This version we use a double value for the height and bias factorPACE=500the frequency for hill additionHEIGHT=2.5the heights of the Gaussian hillsBIASFACTOR=40use well tempered metadynamics and use this bias factorTEMP=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 6.84-7.06the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.5,3.5 # Gaussians will be written to file and also stored on gridthe widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedGRID_WSTRIDE=100000 #GRID_RFILE=grid1.datwrite the grid to a file every N stepsGRID_WFILE=grid1.datthe file on which to write the gridGRID_NOSPLINEdon't use spline interpolation with gridsGRID_MIN=0,-100the lower bounds for the gridGRID_MAX=35,0the upper bounds for the gridGRID_BIN=350,200 ... # Print both collective variables on COLVAR file every 100 stepsthe number of bins for the gridPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5,d6,d7,d8,CV1,CV2,metad.biasFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=100the frequency with which the quantities of interest should be output