Project ID: plumID:21.012
Source: plumed-nest/wild/plumed.dat
Originally used with PLUMED version: 2.7
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
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# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
# COLVAR lig:COMCalculate the center of mass for a group of atoms. More detailsATOMS=5533-5577 # you need the COM of your ligand/molecule pbd1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3261-3284 # describe product binding domain (res 213) pbd2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3736-3756 # describe prroduct binding domain (res 245) wallres:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4335-4349 # lower wall on deep active site residuethe list of atoms which are involved the virtual atom's definition
# FUNNEL wd:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3616,lig # anchor dist for walls fps:the pair of atom that we are calculating the distance betweenFUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More detailsREFERENCE=ref.pdba file in pdb format containing the structure you would like to alignLIGAND=ligThis MUST be a single atom, normally the COM of the ligandANCHOR=3616Closest protein atom to the ligand, picked to avoid pbc problems during the simulationPOINTS=5.1375,4.3952,5.3672,6.5414,3.6569,5.43596 values defining x, y, and z of the 2 points used to construct the line
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=pbd1,lig # For the meta, not Funnel related d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=pbd2,lig d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=wallres,ligthe pair of atom that we are calculating the distance betweenFUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. More detailsARG=fps.lp,fps.ldthe input for this action is the scalar output from one or more other actionsZCC=2.5switching point between cylinder and coneALPHA=0.55angle to change the width of the cone sectionRCYL=0.1radius of the cylindrical sectionMINS=-1minimum value assumed by fpsMAXS=6maximum value assumed by fpsKAPPA=50000constant to be used for the funnel-shape restraint potentialNBINS=500number of bins along fpsNBINZ=500number of bins along fpsSAFETY=1.0To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)SLOPE=1.0Adjust the behavior of the potential outside the funnel, greater values than 1LABEL=funnela label for the action so that its output can be referenced in the input to other actionsFILE=BIASname of the Funnel potential file
### METADYNAMICS ###METAD...Used to performed metadynamics on one or more collective variables. More detailsARG=d1,fps.lpthe input for this action is the scalar output from one or more other actionsSIGMA=0.05,0.05the widths of the Gaussian hillsHEIGHT=2.5 #kj/molthe heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=8use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-0.5,-1the lower bounds for the gridGRID_MAX=5.0,6.0the upper bounds for the gridLABEL=metad # Not Funnel related ... METADa label for the action so that its output can be referenced in the input to other actions
### WALLS ###UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=fps.lpthe arguments on which the bias is actingAT=4.0the positions of the wallKAPPA=500000.0the force constant for the wallEXP=2the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=uwall1a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=fps.ldthe arguments on which the bias is actingAT=1.0the positions of the wallKAPPA=500000.0the force constant for the wallEXP=2the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=uwall2a label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=fps.lpthe arguments on which the bias is actingAT=0.00the positions of the wallKAPPA=500000.0the force constant for the wallEXP=3the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=lwall1a label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=fps.ldthe arguments on which the bias is actingAT=0.0the positions of the wallKAPPA=500000.0the force constant for the wallEXP=3the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=lwall2a label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d3the arguments on which the bias is actingAT=0.7the positions of the wallKAPPA=500000.0the force constant for the wallLABEL=reswalla label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsSTRIDE=1000the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities