**Project ID:** plumID:21.028

**Source:** hBromination/unbiased/reagents/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.

#UNITSUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths

#LOAD FILESLOADLoads a library, possibly defining new actions. More detailsFILE=file to be loaded../../Contacts.cpp

# Atoms labels: [1-c1][2-c2][3-h1][4-h2][5-c5][6-h3][7-h4][8-h5][9-h6][10-b1][11-h7]

# Traditional distancesd1: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 distances

# ========= walls definition ========= # prevent hydrogen moleculesH: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=3,4,6,7,8,9,11the numerical indexes for the set of atoms in the groupdHH:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBHGROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBHMIN={BETA=20}calculate the minimum valueNOPBCignore the periodic boundary conditions when calculating distanceswallHH:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdHHAT=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

# keep COMs nearuwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1,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 wall

# fix hydrogens on C1 -> bonding Br laterald13: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 arguments on which the bias is actingd13,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 wall

# fix hydrogens on C3 -> nonbonding Br laterald57: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 arguments on which the bias is actingd57,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 wall

# fix hydrogen on C2 -> bonding Br centrald26: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 distanceswallCmH1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd26AT=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 wall

# ====== CONTACTS ======= #DEFINE GROUP OF ATOMSC: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=1,2,5 #H: GROUP ATOMS=3,4,6,7,8,9,11the numerical indexes for the set of atoms in the groupBr: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=10the numerical indexes for the set of atoms in the groupcc2:CONTACTSGROUPA=This action is not part of PLUMED and was included by using a LOAD command More detailsCSWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}cb2:CONTACTSGROUPA=This action is not part of PLUMED and was included by using a LOAD command More detailsCGROUPB=BrSWITCH={RATIONAL D_0=0.0 R_0=1.9 NN=6 MM=8}ch2:CONTACTSGROUPA=This action is not part of PLUMED and was included by using a LOAD command More detailsCGROUPB=HSWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}bh2:CONTACTSGROUPA=This action is not part of PLUMED and was included by using a LOAD command More detailsBrGROUPB=HSWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}

# ====== OUTPUT ======Print quantities to a file. More detailsSTRIDE=50the frequency with which the quantities of interest should be outputFILE=distancesthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5Print quantities to a file. More detailsSTRIDE=50the frequency with which the quantities of interest should be outputFILE=contactsthe name of the file on which to output these quantitiesARG=cc2.*,cb2.*,ch2.*,bh2the input for this action is the scalar output from one or more other actions