**Project ID:** plumID:20.024

**Source:** Hydrobromination/static_bias/plumed.dat

**Originally used with PLUMED version:** 2.7

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

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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=../../GAMBES.cppfile to be loadedUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=fsthe units of timed1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,11the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,1the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd4:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd5:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,1the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesene:ENERGYCalculate the total potential energy of the simulation box. More detailss1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5COEFFICIENTS=-0.523,0.726,0.401,-0.029,-0.193the coefficients of the arguments in your functionPOWERS=1,1,1,1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functions2:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5COEFFICIENTS=0.573,-0.339,-0.183,-0.636,-0.345the coefficients of the arguments in your functionPOWERS=1,1,1,1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionGAMBES... ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsd1,d2,d3,d4,d5NSTATES=3 FILENAME=gdist_n PACE=500 LABEL=extBIAS_CUTOFF CUTOFF=150 LAMBDA=0.01 TEMPERATURE=300 STATIC_BIAS STATIC_FACTORS=1,4000,1.0006 ... GAMBES

#..............................WALLS.................................................uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5AT=3.0,3.0,3.0,3.0,3.0the positions of the wallKAPPA=150.0,150.0,150.0,150.0,150.0the force constant for the wallH1: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=3,4the numerical indexes for the set of atoms in the groupH2: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=7,8,9the numerical indexes for the set of atoms in the groupH: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=11the numerical indexes for the set of atoms in the groupC_end:ATOMS=1,5the numerical indexes for the set of atoms in the groupC_mid:ATOMS=2the numerical indexes for the set of atoms in the groupBr:ATOMS=10the numerical indexes for the set of atoms in the groupCe1:ATOMS=1the numerical indexes for the set of atoms in the groupCe2:ATOMS=5the numerical indexes for the set of atoms in the groupH_all:ATOMS=3,4,6,7,8,9,11the numerical indexes for the set of atoms in the groupdCe1H1:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBCe1GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBH1HIGHESTthis flag allows you to recover the highest of these variablesNOPBCignore the periodic boundary conditions when calculating distancesdCe2H2:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBCe2GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBH2HIGHESTthis flag allows you to recover the highest of these variablesNOPBCignore the periodic boundary conditions when calculating distancesdCmH1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,6the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesdHH:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBH_allGROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBH_allMIN={BETA=20}calculate the minimum valueNOPBCignore the periodic boundary conditions when calculating distancesd13:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,3the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd14:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,4the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distanceswallCe1H1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsd13,d14AT=1.4,1.4the positions of the wallKAPPA=150.0,150.0the force constant for the wallEXP=2,2the powers for the wallsEPS=1.0,1.0the values for s_i in the expression for a wallOFFSET=0.2,0.2the offset for the start of the walld57:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,7the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd58:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,8the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesd59:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,9the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distanceswallCe2H2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsd57,d58,d59AT=1.4,1.4,1.4the positions of the wallKAPPA=150.0,150.0,150.0the force constant for the wallEXP=2,2,2the powers for the wallsEPS=1.0,1.0,1.0the values for s_i in the expression for a wallOFFSET=0.2,0.2,0.2the offset for the start of the wallwallCmH1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdCmH1AT=1.4the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsEPS=1.0the values for s_i in the expression for a wallOFFSET=0.2the offset for the start of the wallwallHH:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdHHAT=1.4the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsEPS=1.0 #OFFSET=1.3the values for s_i in the expression for a wall

##################################################Print quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFMT=%8.4f #PRINT ARG=ext.probability.0,ext.probability.1,ext.probability.2 STRIDE=10 FILE=GAMBES FMT=%8.10fthe format that should be used to output real numbers