**Project ID:** plumID:21.042

**Source:** Plumed_nest/plumed_Nce6Ncp6_Au111.dat

**Originally used with PLUMED version:** 2.4

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

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

## RESTARTMOLINFOThis 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=Nce6Ncp6.pdba file in pdb format containing a reference structure

## ENERGY LABEL=energybb:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7201,7203,7206,7225,7226,7229,7248,7249,7252,7271,7272,7275,7294,7295,7298,7317,7318,7321,7340,7341,7344,7355,7356,7359,7370,7371,7374,7385,7386,7389,7400,7401,7404,7415,7416,7419the list of atoms which are involved the virtual atom's definitionpr1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7211,7214-7224the list of atoms which are involved the virtual atom's definitionpr2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7234,7237-7247the list of atoms which are involved the virtual atom's definitionpr3:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7257,7260-7270the list of atoms which are involved the virtual atom's definitionpr4:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7280,7283-7293the list of atoms which are involved the virtual atom's definitionpr5:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7303,7306-7316the list of atoms which are involved the virtual atom's definitionpr6:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7326,7329-7339the list of atoms which are involved the virtual atom's definitioncc1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7346-7354the list of atoms which are involved the virtual atom's definitioncc2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7361-7369the list of atoms which are involved the virtual atom's definitioncc3:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7376-7384the list of atoms which are involved the virtual atom's definitioncc4:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7391-7399the list of atoms which are involved the virtual atom's definitioncc5:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7406-7414the list of atoms which are involved the virtual atom's definitioncc6:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7421-7429the list of atoms which are involved the virtual atom's definition

## com: COM ATOMS=7201-7432dbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenbbCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr1COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr2COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr3COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr4:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr4COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr5:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr5COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpr6:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweenpr6COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc1COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc2COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc3COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc4:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc4COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc5:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc5COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdcc6:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,the pair of atom that we are calculating the distance betweencc6COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distances

## dcom: DISTANCE ATOMS=7200,com COMPONENTS NOPBCUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdbb.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dbbUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr1.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr1UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr2.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr3.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr3UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr4.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr4UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr5.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr5UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdpr6.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpr6UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc1.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc1UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc2.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc3.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc3UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc4.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc4UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc5.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc5UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdcc6.zAT=8.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dcc6GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=7201-7432the group of atoms that you are calculating the Gyration Tensor forLABEL=a label for the action so that its output can be referenced in the input to other actionsrgPBMETAD...Used to performed Parallel Bias metadynamics. More detailsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRARG=the input for this action is the scalar output from one or more other actionsdbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.z,rgSIGMA=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02the widths of the Gaussian hillsHEIGHT=1.2 #kJ/molthe height of the Gaussian hills, one for all biasesPACE=500the frequency for hill addition, one for all biasesBIASFACTOR=20use well tempered metadynamics with this bias factor, one for all biasesTEMP=298.0the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=a label for the action so that its output can be referenced in the input to other actionsPBMETADGRID_MIN=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0the lower bounds for the gridGRID_MAX=8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,7the upper bounds for the gridFILE=HILLS.dbb,HILLS.dpr1,HILLS.dpr2,HILLS.dpr3,HILLS.dpr4,HILLS.dpr5,HILLS.dpr6,HILLS.dcc1,HILLS.dcc2,HILLS.dcc3,HILLS.dcc4,HILLS.dcc5,HILLS.dcc6,HILLS.rg ... PBMETADfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsPBMETAD.bias,dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.z,rgSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities