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
Click on the labels of the actions for more information on what each action computes
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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 performed
rmsd_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=OPTIMAL rmsd_wat:the manner in which RMSD alignment is performedRMSDCalculate 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=OPTIMAL rmsd_sub:the manner in which RMSD alignment is performedRMSDCalculate 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=OPTIMAL rmsd_all:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=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 performed
h: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=473,484,485,30,102,123,33,2,120,481,482 o_ph:the numerical indexes for the set of atoms in the groupGROUPDefine 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=29,101,122,32,119,1 o_w1:the numerical indexes for the set of atoms in the groupGROUPDefine 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=483 o_w2:the numerical indexes for the set of atoms in the groupGROUPDefine 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=480 o_me:the numerical indexes for the set of atoms in the groupGROUPDefine 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=472 cl:the numerical indexes for the set of atoms in the groupGROUPDefine 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=455 gly:the numerical indexes for the set of atoms in the groupGROUPDefine 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=448,447,454,457,458,438,437,440,441,463the numerical indexes for the set of atoms in the group
d_clo:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=455,480 d_oho:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,483 d_ocl:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,454 d_clc:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=455,454 d_mec:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=472,454 d_hgc:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=456,454 d_hgc2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=459,458 d_w2ph1:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=o_w2,1 d_w2ph2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=o_w2,119 b_clo:the pair of atom that we are calculating the distance betweenBRIDGECalculate 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=hThe list of atoms that can form the bridge between the two interesting parts of the structureGROUPA=clGROUPB=o_w2SWITCH={RATIONAL R_0=1.5} b_oho:The parameters of the two switchingfunction in the above formulaBRIDGECalculate 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=hThe list of atoms that can form the bridge between the two interesting parts of the structureGROUPA=o_meGROUPB=o_w1SWITCH={RATIONAL R_0=1.5} b_clm:The parameters of the two switchingfunction in the above formulaBRIDGECalculate 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=hThe list of atoms that can form the bridge between the two interesting parts of the structureGROUPA=clGROUPB=o_w1SWITCH={RATIONAL R_0=2.0} b_clg:The parameters of the two switchingfunction in the above formulaBRIDGECalculate 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=hThe list of atoms that can form the bridge between the two interesting parts of the structureGROUPA=clGROUPB=glySWITCH={RATIONAL R_0=2.0} b_clp:The parameters of the two switchingfunction in the above formulaBRIDGECalculate 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=hThe list of atoms that can form the bridge between the two interesting parts of the structureGROUPA=clGROUPB=o_phSWITCH={RATIONAL R_0=2.0}The parameters of the two switchingfunction in the above formula
c_o_w1h:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=o_w1First list of atomsGROUPB=hSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.5 c_o_meh:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=o_meFirst list of atomsGROUPB=hSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.5 c_h_cl:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=clFirst list of atomsGROUPB=hSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=2.0The r_0 parameter of the switching function
diff:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d_clc,d_mecthe input to this functionCOEFFICIENTS=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 function
prod:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=c_o_w1h,c_o_mehthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
a:ANGLECalculate an angle. More detailsATOMS=455,454,472 a1:the list of atoms involved in this collective variable (either 3 or 4 atoms)ANGLECalculate an angle. More detailsATOMS=480,455,454 a2:the list of atoms involved in this collective variable (either 3 or 4 atoms)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 GROUPBMEANdch2:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch3:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch4:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch5:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch6:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch7:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdch8:calculate the mean of all the quantitiesDISTANCESCalculate 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 quantities
dco1:DISTANCESCalculate 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 GROUPBMEANdco2:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdco3:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdco4:calculate the mean of all the quantitiesDISTANCESCalculate 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 GROUPBMEANdco5:calculate the mean of all the quantitiesDISTANCESCalculate 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 quantities
uwall_1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_clothe arguments on which the bias is actingAT=2.5the positions of the wallKAPPA=200 uwall_2:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_ohothe arguments on which the bias is actingAT=2.5the positions of the wallKAPPA=200 uwall_6:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsd_allthe arguments on which the bias is actingAT=0.0the positions of the wallKAPPA=25000 uwall_7:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=b_clothe arguments on which the bias is actingAT=+0.5the positions of the wallKAPPA=700 uwall_8:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=b_ohothe arguments on which the bias is actingAT=+0.5the positions of the wallKAPPA=700 uwall_10:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=prodthe arguments on which the bias is actingAT=+2.5the positions of the wallKAPPA=200 uwall_11:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=prodthe arguments on which the bias is actingAT=+2.0the positions of the wallKAPPA=150 uwall_12:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diffthe arguments on which the bias is actingAT=+2.5the positions of the wallKAPPA=150 #modifed from +3.5 uwall_13:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diffthe arguments on which the bias is actingAT=-2.5the positions of the wallKAPPA=200 #modifed from -3.5 uwall_15:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=c_h_clthe arguments on which the bias is actingAT=+1.1the positions of the wallKAPPA=300 uwall_16:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=b_clmthe arguments on which the bias is actingAT=+0.0the positions of the wallKAPPA=700 uwall_17:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=b_clgthe arguments on which the bias is actingAT=+0.1the positions of the wallKAPPA=700 uwall_18:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=b_clpthe arguments on which the bias is actingAT=+0.1the positions of the wallKAPPA=700 uwall_19:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_w2ph1the arguments on which the bias is actingAT=+2.4the positions of the wallKAPPA=200 uwall_20:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_w2ph2the arguments on which the bias is actingAT=+2.4the positions of the wallKAPPA=200 uwall_21:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_hgcthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_22:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d_hgc2the arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200the force constant for the wall
auwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=athe arguments on which the bias is actingAT=+2.6281the positions of the wallKAPPA=400 a1uwall:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=a1the arguments on which the bias is actingAT=+2.0699the positions of the wallKAPPA=400 a2uwall:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=a2the arguments on which the bias is actingAT=+1.9018the positions of the wallKAPPA=400the force constant for the wall
alwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=athe arguments on which the bias is actingAT=+2.6281the positions of the wallKAPPA=400 a1lwall:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=a1the arguments on which the bias is actingAT=+2.0699the positions of the wallKAPPA=400 a2lwall:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=a2the arguments on which the bias is actingAT=+1.9018the positions of the wallKAPPA=400the force constant for the wall
uwall_dch1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch1.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch2:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch2.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch3:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch3.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch4:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch4.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch5:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch5.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch6:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch6.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch7:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch7.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200 uwall_dch8:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dch8.meanthe arguments on which the bias is actingAT=+1.0the positions of the wallKAPPA=200the force constant for the wall
uwall_dco1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dco1.meanthe arguments on which the bias is actingAT=+1.4the positions of the wallKAPPA=200 uwall_dco2:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dco2.meanthe arguments on which the bias is actingAT=+1.4the positions of the wallKAPPA=200 uwall_dco3:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dco3.meanthe arguments on which the bias is actingAT=+1.4the positions of the wallKAPPA=200 uwall_dco4:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dco4.meanthe arguments on which the bias is actingAT=+1.4the positions of the wallKAPPA=200 uwall_dco5:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dco5.meanthe arguments on which the bias is actingAT=+1.4the positions of the wallKAPPA=200the force constant for the wallMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=diffthe input for this action is the scalar output from one or more other actionsPACE=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=diff,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,metadthe input for this action is the scalar output from one or more other actionsFLUSHThis 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