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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=GMXfiles/ala3.pdb

FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1

ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c1
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c3
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c5
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c2
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c4
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c6

COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=sum_abs ARGthe values input to this function=c1,c2,c3,c4,c5,c6 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=0.6228,0.1201,0.5643,0.1102,0.5153,0.0403 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=sum_abs HEIGHTthe heights of the Gaussian hills=0.4 BIASFACTORuse well tempered metadynamics and use this bias factor=4 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 SIGMAthe widths of the Gaussian hills=0.04 GRID_MINthe lower bounds for the grid=-0.02 GRID_MAXthe upper bounds for the grid=2.0 GRID_BINthe number of bins for the grid=200 LABELa label for the action so that its output can be referenced in the input to other actions=WTMetaD FREQUENCY_ADAPTIVE Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor PACEthe frequency for hill addition=1000 # 2ps FA_MAX_PACEthe maximum hill addition frequency allowed in frequency adaptive metadynamics=100000 # 200ps FA_UPDATE_FREQUENCYthe frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE=500 FA_MIN_ACCELERATIONonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here=1e1 # enable the update of frq only after reaching a minimum alpha ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor ... METAD
COMMITTORDoes a committor analysis. More details ... ARGthe labels of the values which is being used to define the committor surface=sum_abs STRIDE the frequency with which the CVs are analyzed=5000 BASIN_LL1List of lower limits for basin #=1.85 BASIN_UL1List of upper limits for basin #=2.0 ... COMMITTOR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=sum_abs,WTMetaD.* FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%12.5f