Project ID: plumID:21.042
Source: Plumed_nest/plumed_Nce3Ncp6_Au100.dat
Originally used with PLUMED version: 2.4
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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## 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=Nce3Ncp6.pdba file in pdb format containing a reference structure
## ENERGY LABEL=energy
bb: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 pr1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7211,7214-7224 pr2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7234,7237-7247 pr3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7257,7260-7270 pr4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7280,7283-7293 pr5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7303,7306-7316 pr6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7326,7329-7339 cc1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7346-7354 cc2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7361-7369 cc3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7376-7384the list of atoms which are involved the virtual atom's definition
## com: COM ATOMS=7201-7387
dbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,bbthe pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr4the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr5the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdpr6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,pr6the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdcc1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,cc1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdcc2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,cc2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdcc3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7200,cc3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate 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=dbb.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dbba 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=dpr1.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr1a 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=dpr2.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr2a 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=dpr3.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr3a 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=dpr4.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr4a 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=dpr5.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr5a 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=dpr6.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dpr6a 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=dcc1.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dcc1a 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=dcc2.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dcc2a 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=dcc3.zthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dcc3a label for the action so that its output can be referenced in the input to other actionsGYRATIONCalculate 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=7201-7387the group of atoms that you are calculating the Gyration Tensor forLABEL=rga label for the action so that its output can be referenced in the input to other actionsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRARG=dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,rgthe input for this action is the scalar output from one or more other actionsSIGMA=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=PBMETADa label for the action so that its output can be referenced in the input to other actionsGRID_MIN=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=8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,7the 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.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=PBMETAD.bias,dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,rgthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities