Project ID: plumID:19.083
Source: Reaction_discovery/2.ICl/step2/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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RESTARTActivate restart. More detailsUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
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=1,2 I: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=3,5 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=4,6the 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 matrixMEANII: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=Ithis keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=0.0 R_0=3.0 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMEANClCl: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=Clthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=0.0 R_0=2.3 NN=6 MM=8}the switching function that it used in the construction of the contact matrixMEANHCl: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=Hthis keyword is used for colvars such as the coordination numberSPECIESB=Clthis 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} ClH:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Clthis 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=1.6 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} HI: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=Ithis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.9 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} IH:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Ithis 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=1.9 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} ICl:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Ithis keyword is used for colvars such as the coordination numberSPECIESB=Clthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=2.6 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} ClI:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Clthis keyword is used for colvars such as the coordination numberSPECIESB=Ithis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=2.6 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}calculate the maximum value
d1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=hh.meanthe input to this functionCOEFFICIENTS=1.0232the 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=II.meanthe input to this functionCOEFFICIENTS=1.1790the 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=ClCl.meanthe input to this functionCOEFFICIENTS=2.1364the 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=HCl.maxthe input to this functionCOEFFICIENTS=0.7082the 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=HCl.minthe input to this functionCOEFFICIENTS=0.8116the 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=ClH.maxthe input to this functionCOEFFICIENTS=0.6879the 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=ClH.minthe input to this functionCOEFFICIENTS=0.7994the 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=HI.maxthe input to this functionCOEFFICIENTS=1.1615the 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=HI.minthe input to this functionCOEFFICIENTS=1.7905the 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=IH.maxthe input to this functionCOEFFICIENTS=1.2714the 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=IH.minthe input to this functionCOEFFICIENTS=1.6849the 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=ICl.maxthe input to this functionCOEFFICIENTS=0.8310the 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=ICl.minthe input to this functionCOEFFICIENTS=0.9355the 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=ClI.maxthe input to this functionCOEFFICIENTS=0.8257the 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=ClI.minthe input to this functionCOEFFICIENTS=0.9352the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
sdg1full: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=0.6688,-0.0250,-0.2889,-0.3031,-0.5252,0.2230,-0.1102,-0.0069,0.0331,-0.0102,-0.0103,0.1540,-0.0335,0.0968,0.0583the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
svd13: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=0.7435,-0.0278,-0.3230,0.0052,-0.4295,-0.0315,-0.3276,-0.0540,0.0093,0.0297,0.0162,0.1870,-0.0130,0.0911,0.0412the coefficients of the arguments in your functionPERIODIC=NO svd11: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=0.7739,-0.0297,-0.3295,-0.1430,-0.2591,-0.0257,-0.3954,-0.0026,0.0093,0.0020,-0.0007,0.1858,-0.0170,0.0995,0.0471the coefficients of the arguments in your functionPERIODIC=NO svd9: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=0.8395,-0.0959,-0.0923,-0.2187,-0.0523,-0.0162,-0.3158,-0.0256,0.0579,0.0008,0.0004,0.0280,0.2146,-0.0464,0.2719the coefficients of the arguments in your functionPERIODIC=NO svd7: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=-0.0743,-0.1207,-0.1905,-0.1565,-0.2149,0.0360,-0.4456,0.1727,-0.1967,0.0591,0.0559,0.0772,0.4405,-0.1388,0.6154the coefficients of the arguments in your functionPERIODIC=NO svd5: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=-0.0223,-0.1612,0.2841,-0.2182,-0.1949,-0.3663,-0.0153,-0.0309,0.0018,0.0264,-0.0796,0.4268,0.3542,0.5620,0.2033the coefficients of the arguments in your functionPERIODIC=NO svd3: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=-0.0043,0.3781,-0.0278,-0.3167,-0.2908,-0.6031,0.0578,0.0246,0.1205,-0.2184,0.4635,0.0417,0.0964,0.0185,0.1236the coefficients of the arguments in your functionPERIODIC=NO svd1: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=-0.0170,0.0092,-0.2062,-0.1258,-0.1245,-0.1567,-0.0838,0.1953,-0.1107,0.1000,0.0367,0.5470,0.3433,0.5465,0.3417the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
sdg1filter095: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=0.7429,-0.0276,-0.3225,0.0,-0.4192,-0.0218,-0.3448,-0.0248,0.0316,0.0,-0.0045,0.1832,-0.0276,0.0958,0.0550the coefficients of the arguments in your functionPERIODIC=NO sdg1filter090: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=0.7026,-0.0342,-0.3478,0.0,-0.3629,0.0,-0.3840,-0.0031,0.0186,0.0,-0.0052,0.2806,0.1303,0.0,-0.0945the coefficients of the arguments in your functionPERIODIC=NO sdg1filter080: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=0.7129,-0.0308,-0.3414,0.0,-0.3708,0.0,-0.3858,0.0,0.0141,0.0,0.0,0.2963,0.0,0.0,-0.0026the coefficients of the arguments in your functionPERIODIC=NO sdg1filter070: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=0.6918,-0.0317,-0.3351,0.0,-0.5711,0.0,0.0,0.0,-0.0040,0.0,0.0,0.2864,0.0,0.0,0.0036the coefficients of the arguments in your functionPERIODIC=NO sdg1filter060: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=0.7606,-0.0474,-0.0355,0.0,-0.6226,0.0,0.0,0.0,-0.0050,0.0,0.0,0.0,0.0,0.0,0.1741the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
dHCl:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=HCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=ClCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCdHI:ignore the periodic boundary conditions when calculating distancesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=HCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=ICalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCdICl:ignore the periodic boundary conditions when calculating distancesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=ICalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=ClCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.02}calculate the maximum valueNOPBCwallHCl:ignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dHCl.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 wallHI: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=dHI.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 wallICl: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=dICl.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=1.5the 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