**Project ID:** plumID:22.009

**Source:** plumed.dat

**Originally used with PLUMED version:** 2.5

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

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

UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=0.001the units of timeWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-432the atoms that make up a molecule that you wish to alignENTITY1=433-442the atoms that make up a molecule that you wish to alignENTITY2=449-451the atoms that make up a molecule that you wish to alignENTITY3=452-454the atoms that make up a molecule that you wish to alignENTITY4=455-457the atoms that make up a molecule that you wish to alignENTITY5=458-460the atoms that make up a molecule that you wish to alignENTITY6=461-463the atoms that make up a molecule that you wish to alignENTITY7=464-466the atoms that make up a molecule that you wish to alignENTITY8=467-469the atoms that make up a molecule that you wish to alignENTITY9=470-472the atoms that make up a molecule that you wish to alignFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsREFERENCE=heavy_atoms.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedrmsd_cal:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=heavy_atoms_cal.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedrmsd_wat:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=heavy_atoms_wat.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedrmsd_sub:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=heavy_atoms_sub.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedrmsd_all:REFERENCE=heavy_atoms_npt_sel.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedh:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=473,484,485,30,102,123,33,2,120,481,482the numerical indexes for the set of atoms in the groupo_ph:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=29,101,122,32,119,1the numerical indexes for the set of atoms in the groupo_w1:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=483the numerical indexes for the set of atoms in the groupo_w2:ATOMS=480the numerical indexes for the set of atoms in the groupo_me:ATOMS=472the numerical indexes for the set of atoms in the groupcl:ATOMS=455the numerical indexes for the set of atoms in the groupgly:ATOMS=448,447,454,457,458,438,437,440,441,463the numerical indexes for the set of atoms in the groupd_clo:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=455,480the pair of atom that we are calculating the distance betweend_oho:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,483the pair of atom that we are calculating the distance betweend_ocl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,454the pair of atom that we are calculating the distance betweend_clc:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=455,454the pair of atom that we are calculating the distance betweend_mec:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,454the pair of atom that we are calculating the distance betweend_hgc:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=456,454the pair of atom that we are calculating the distance betweend_hgc2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=459,458the pair of atom that we are calculating the distance betweend_w2ph1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweeno_w2,1d_w2ph2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweeno_w2,119b_clo:BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More detailsBRIDGING_ATOMS=The list of atoms that can form the bridge between the two interesting parts of the structurehGROUPA=clGROUPB=o_w2SWITCH={RATIONAL R_0=1.5}The parameters of the two switchingfunction in the above formulab_oho:BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More detailsBRIDGING_ATOMS=The list of atoms that can form the bridge between the two interesting parts of the structurehGROUPA=o_meGROUPB=o_w1SWITCH={RATIONAL R_0=1.5}The parameters of the two switchingfunction in the above formulab_clm:BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More detailsBRIDGING_ATOMS=The list of atoms that can form the bridge between the two interesting parts of the structurehGROUPA=clGROUPB=o_w1SWITCH={RATIONAL R_0=2.0}The parameters of the two switchingfunction in the above formulab_clg:The list of atoms that can form the bridge between the two interesting parts of the structurehGROUPA=clGROUPB=glySWITCH={RATIONAL R_0=2.0}The parameters of the two switchingfunction in the above formulab_clp:The list of atoms that can form the bridge between the two interesting parts of the structurehGROUPA=clGROUPB=o_phSWITCH={RATIONAL R_0=2.0}The parameters of the two switchingfunction in the above formulac_o_w1h:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=First list of atomso_w1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)hR_0=1.5The r_0 parameter of the switching functionc_o_meh:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=First list of atomso_meGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)hR_0=1.5The r_0 parameter of the switching functionc_h_cl:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=First list of atomsclGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)hR_0=2.0The r_0 parameter of the switching functiondiff:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond_clc,d_mecCOEFFICIENTS=1,-1the coefficients of the arguments in your functionPERIODIC=NO #NORMALIZEif the output of your function is periodic then you should specify the periodicity of the functionprod:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=the input to this functionc_o_w1h,c_o_mehFUNC=x*ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functiona:ANGLECalculate an angle. More detailsATOMS=455,454,472the list of atoms involved in this collective variable (either 3 or 4 atoms)a1:ANGLECalculate an angle. More detailsATOMS=480,455,454the list of atoms involved in this collective variable (either 3 or 4 atoms)a2:ANGLECalculate an angle. More detailsATOMS=454,472,483the list of atoms involved in this collective variable (either 3 or 4 atoms)dch1:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=464Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=465,466,467Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch2:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=460Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=461,462Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch3:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=433Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=435,436,434Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch4:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=438Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=439Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch5:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=442Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=445,443,444Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch6:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=454Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=456Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch7:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=447Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=453Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdch8:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=449Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=450,451,452Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdco1:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=454,458Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=457Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdco2:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=464,460Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=463Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdco3:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=433,438Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=437Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdco4:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=440,442Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=441Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesdco5:Calculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=447,449Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=448Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMEANcalculate the mean of all the quantitiesuwall_1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_cloAT=2.5the positions of the wallKAPPA=200the force constant for the walluwall_2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_ohoAT=2.5the positions of the wallKAPPA=200the force constant for the walluwall_6:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingrmsd_allAT=0.0the positions of the wallKAPPA=25000the force constant for the walluwall_7:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingb_cloAT=+0.5the positions of the wallKAPPA=700the force constant for the walluwall_8:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingb_ohoAT=+0.5the positions of the wallKAPPA=700the force constant for the walluwall_10:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingprodAT=+2.5the positions of the wallKAPPA=200the force constant for the walluwall_11:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingprodAT=+2.0the positions of the wallKAPPA=150the force constant for the walluwall_12:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdiffAT=+2.5the positions of the wallKAPPA=150 #modifed from +3.5the force constant for the walluwall_13:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdiffAT=-2.5the positions of the wallKAPPA=200 #modifed from -3.5the force constant for the walluwall_15:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingc_h_clAT=+1.1the positions of the wallKAPPA=300the force constant for the walluwall_16:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingb_clmAT=+0.0the positions of the wallKAPPA=700the force constant for the walluwall_17:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingb_clgAT=+0.1the positions of the wallKAPPA=700the force constant for the walluwall_18:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingb_clpAT=+0.1the positions of the wallKAPPA=700the force constant for the walluwall_19:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_w2ph1AT=+2.4the positions of the wallKAPPA=200the force constant for the walluwall_20:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_w2ph2AT=+2.4the positions of the wallKAPPA=200the force constant for the walluwall_21:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_hgcAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_22:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd_hgc2AT=+1.0the positions of the wallKAPPA=200the force constant for the wallauwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingaAT=+2.6281the positions of the wallKAPPA=400the force constant for the walla1uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actinga1AT=+2.0699the positions of the wallKAPPA=400the force constant for the walla2uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actinga2AT=+1.9018the positions of the wallKAPPA=400the force constant for the wallalwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingaAT=+2.6281the positions of the wallKAPPA=400the force constant for the walla1lwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actinga1AT=+2.0699the positions of the wallKAPPA=400the force constant for the walla2lwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actinga2AT=+1.9018the positions of the wallKAPPA=400the force constant for the walluwall_dch1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch1.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch2.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch3:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch3.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch4:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch4.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch5:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch5.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch6:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch6.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch7:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch7.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dch8:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdch8.meanAT=+1.0the positions of the wallKAPPA=200the force constant for the walluwall_dco1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdco1.meanAT=+1.4the positions of the wallKAPPA=200the force constant for the walluwall_dco2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdco2.meanAT=+1.4the positions of the wallKAPPA=200the force constant for the walluwall_dco3:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdco3.meanAT=+1.4the positions of the wallKAPPA=200the force constant for the walluwall_dco4:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdco4.meanAT=+1.4the positions of the wallKAPPA=200the force constant for the walluwall_dco5:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdco5.meanAT=+1.4the positions of the wallKAPPA=200the force constant for the wallMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsmetadARG=the input for this action is the scalar output from one or more other actionsdiffPACE=100the frequency for hill additionHEIGHT=3.0the heights of the Gaussian hillsSIGMA=0.05the widths of the Gaussian hillsBIASFACTOR=50use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsFILE=HILLSa file in which the list of added hills is storedGRID_MIN=-9.0the lower bounds for the gridGRID_MAX=9the upper bounds for the gridGRID_BIN=200the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print quantities to a file. More detailsFILE=COLVARthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsdiff,d_clo,d_oho,d_ocl,rmsd_cal,rmsd_wat,rmsd_sub,rmsd_all,prod,b_clo,b_oho,b_clm,prod,a,c_h_cl,metadFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1the frequency with which all the open files should be flushed