**Project ID:** plumID:19.019

**Source:** FA-MetaD-Ala3-plumed/plumed_FaMetaD.dat

**Originally used with PLUMED version:** 2.5

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

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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=GMXfiles/ala3.pdba file in pdb format containing a reference structureFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1the frequency with which all the open files should be flushedALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More detailsATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc1ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More detailsATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc3ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More detailsATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc5ATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc2ATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc4ATOMS1=the atoms involved in each of the alpha-beta variables you wish to calculate@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.REFERENCE=1.25the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsc6COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionssum_absARG=the input for this action is the scalar output from one or more other actionsc1,c2,c3,c4,c5,c6POWERS=1,1,1,1,1,1the powers to which you are raising each of the arguments in your functionCOEFFICIENTS=0.6228,0.1201,0.5643,0.1102,0.5153,0.0403the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionMETAD...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 actionssum_absHEIGHT=0.4the heights of the Gaussian hillsBIASFACTOR=4use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.04the widths of the Gaussian hillsGRID_MIN=-0.02the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=200the number of bins for the gridLABEL=a label for the action so that its output can be referenced in the input to other actionsWTMetaDFREQUENCY_ADAPTIVESet to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factorPACE=1000 # 2psthe frequency for hill additionFA_MAX_PACE=100000 # 200psthe maximum hill addition frequency allowed in frequency adaptive metadynamicsFA_UPDATE_FREQUENCY=500the frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACEFA_MIN_ACCELERATION=1e1 # enable the update of frq only after reaching a minimum alphaonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given hereACCELERATION... METADSet to TRUE if you want to compute the metadynamics acceleration factorCOMMITTOR...Does a committor analysis. More detailsARG=the input for this action is the scalar output from one or more other actionssum_absSTRIDE=5000the frequency with which the CVs are analyzedBASIN_LL1=1.85List of lower limits for basin #BASIN_UL1=2.0 ... COMMITTORList of upper limits for basin #Print quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARG=the input for this action is the scalar output from one or more other actionssum_abs,WTMetaDFILE=COLVARthe name of the file on which to output these quantitiesFMT=%12.5fthe format that should be used to output real numbers