Project ID: plumID:19.083
Source: Reaction_discovery/1.H2_NO/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
RESTARTActivate restart. More detailsUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
N: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=1,3 O: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=2,4 H: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=5,6,7,8the numerical indexes for the set of atoms in the group
hh:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIES=Hthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMEANnn:calculate the mean of all the quantitiesCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIES=Nthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.5 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMEANoo:calculate the mean of all the quantitiesCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIES=Othis keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMEANno:calculate the mean of all the quantitiesCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Nthis keyword is used for colvars such as the coordination numberSPECIESB=Othis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02} on:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Othis keyword is used for colvars such as the coordination numberSPECIESB=Nthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02} nh:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Nthis keyword is used for colvars such as the coordination numberSPECIESB=Hthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02} hn:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Hthis keyword is used for colvars such as the coordination numberSPECIESB=Nthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02} oh:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Othis keyword is used for colvars such as the coordination numberSPECIESB=Hthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02} ho:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Hthis keyword is used for colvars such as the coordination numberSPECIESB=Othis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMIN={BETA=20.0}calculate the minimum valueMAX={BETA=0.02}calculate the maximum value
d1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=hh.meanthe input to this functionCOEFFICIENTS=1.00the coefficients of the arguments in your functionPERIODIC=NO d2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nn.meanthe input to this functionCOEFFICIENTS=1.0734the coefficients of the arguments in your functionPERIODIC=NO d3:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=oo.meanthe input to this functionCOEFFICIENTS=1.6782the coefficients of the arguments in your functionPERIODIC=NO d4:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=no.maxthe input to this functionCOEFFICIENTS=0.7097the coefficients of the arguments in your functionPERIODIC=NO d5:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=no.minthe input to this functionCOEFFICIENTS=0.7637the coefficients of the arguments in your functionPERIODIC=NO d6:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=on.maxthe input to this functionCOEFFICIENTS=0.7121the coefficients of the arguments in your functionPERIODIC=NO d7:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=on.minthe input to this functionCOEFFICIENTS=0.7643the coefficients of the arguments in your functionPERIODIC=NO d8:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nh.maxthe input to this functionCOEFFICIENTS=0.9618the coefficients of the arguments in your functionPERIODIC=NO d9:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nh.minthe input to this functionCOEFFICIENTS=1.1010the coefficients of the arguments in your functionPERIODIC=NO d10:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=hn.maxthe input to this functionCOEFFICIENTS=1.3052the coefficients of the arguments in your functionPERIODIC=NO d11:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=hn.minthe input to this functionCOEFFICIENTS=2.5949the coefficients of the arguments in your functionPERIODIC=NO d12:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=oh.maxthe input to this functionCOEFFICIENTS=0.3617the coefficients of the arguments in your functionPERIODIC=NO d13:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=oh.minthe input to this functionCOEFFICIENTS=0.4227the coefficients of the arguments in your functionPERIODIC=NO d14:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ho.maxthe input to this functionCOEFFICIENTS=0.6276the coefficients of the arguments in your functionPERIODIC=NO d15:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ho.minthe input to this functionCOEFFICIENTS=0.8866the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
#the following are 32,33,34 svd14:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15the input to this functionCOEFFICIENTS=0.0,-0.02114,0.00334,-0.23391,-0.64088,0.21637,0.69767,0.00113,-0.00213,-0.00001,0.00025,0.00206,-0.00739,-0.00457,-0.02124the coefficients of the arguments in your functionPERIODIC=NO svd13:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15the input to this functionCOEFFICIENTS=0.0,-0.39547,0.06121,-0.20744,0.60671,-0.11341,0.47938,0.02201,-0.03897,-0.00129,0.00439,0.03726,-0.13914,-0.08409,-0.39524the coefficients of the arguments in your functionPERIODIC=NO svd12:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15the input to this functionCOEFFICIENTS=0.0,-0.40711,0.06514,-0.17925,0.61216,-0.15080,0.50432,0.02309,-0.04043,-0.00128,0.00438,-0.02035,-0.27076,-0.03965,-0.26189the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
dNN:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=NCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=NCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCdNH:ignore the periodic boundary conditions when calculating distancesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=NCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=HCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCdOO:ignore the periodic boundary conditions when calculating distancesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=OCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=OCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCwallNN:ignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dNN.maxthe arguments on which the bias is actingAT=9.0the positions of the wallKAPPA=200.0the force constant for the wallEXP=2the powers for the wallsEPS=1 wallNH:the values for s_i in the expression for a wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dNH.maxthe arguments on which the bias is actingAT=9.0the positions of the wallKAPPA=200.0the force constant for the wallEXP=2the powers for the wallsEPS=1 wallNaN:the values for s_i in the expression for a wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dOO.maxthe arguments on which the bias is actingAT=9.0the positions of the wallKAPPA=200.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=svd13the input for this action is the scalar output from one or more other actionsSIGMA=0.05the widths of the Gaussian hillsHEIGHT=3.0the heights of the Gaussian hillsPACE=100the frequency for hill additionLABEL=restraint ... METADa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=20the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=20the frequency with which all the open files should be flushedENDPLUMEDTerminate plumed input. More details