Project ID: plumID:23.018
Source: Z2_Au111/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# # RESTART
# # MOLINFO MOLTYPE=protein STRUCTURE=conf.pdb # # ENERGY LABEL=energy
# N,CA,C,O bb:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7201,7204,7224,7225,7226,7228,7241,7242,7243,7245,7265,7266,7267,7269,7282,7283,7284,7286,7304,7305,7306,7308,7321,7322,7323,7325,7343,7344the list of atoms which are involved the virtual atom's definition
# CB and on for sidechain headgoups res1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7206-7223 res2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7230-7240 res3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7247-7264 res4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7271-7281 res5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7288-7303 res6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7310-7320 res7:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=7327-7342the list of atoms which are involved the virtual atom's definition
surf:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7200the list of atoms which are involved the virtual atom's definition
dbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,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 labelNOPBCdres1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res4the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res5the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res6the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdres7:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,res7the 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 distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dbb.zthe arguments on which the bias is actingAT=5.5the 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=dres1.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres1a 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=dres2.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres2a 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=dres3.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres3a 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=dres4.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres4a 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=dres5.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres5a 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=dres6.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres6a 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=dres7.zthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dres7a label for the action so that its output can be referenced in the input to other actions
# all atomsGYRATIONCalculate 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=7201-7346the 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,dres1.z,dres2.z,dres3.z,dres4.z,dres5.z,dres6.z,dres7.z,rgthe input for this action is the scalar output from one or more other actionsSIGMA=200.0the widths of the Gaussian hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4the upper bounds for the sigmas (in CV units) when using adaptive hillsHEIGHT=1.2 #kJ/molthe height of the Gaussian hills, one for all biasesPACE=500the frequency for hill addition, one for all biasesBIASFACTOR=24 # Sqrt[cv]*8use 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=-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,0.0the lower bounds for the gridGRID_MAX=7.5,7.5,7.5,7.5,7.5,7.5,7.5,7.5,7.0the upper bounds for the gridFILE=../HILLS.dbb,../HILLS.dres1,../HILLS.dres2,../HILLS.dres3,../HILLS.dres4,../HILLS.dres5,../HILLS.dres6,../HILLS.dres7,../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,dres1.z,dres2.z,dres3.z,dres4.z,dres5.z,dres6.z,dres7.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