Project ID: plumID:20.024
Source: Hydrobromination/known_propene/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

Click on the labels of the actions for more information on what each action computes
```# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs
d1:  DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances
d2:  DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1 NOPBC ignore the periodic boundary conditions when calculating distances
d3:  DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 NOPBC ignore the periodic boundary conditions when calculating distances
d4:  DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2 NOPBC ignore the periodic boundary conditions when calculating distances
d5:  DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 NOPBC ignore the periodic boundary conditions when calculating distances
ene: ENERGYCalculate the total potential energy of the simulation box. More details
s1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe input for this action is the scalar output from one or more other actions=d1,d2,d3,d4,d5 COEFFICIENTS the coefficients of the arguments in your function=-0.523,0.726,0.401,-0.029,-0.193 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
s2: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe input for this action is the scalar output from one or more other actions=d1,d2,d3,d4,d5 COEFFICIENTS the coefficients of the arguments in your function=0.573,-0.339,-0.183,-0.636,-0.345 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
GAMBESThis action is not part of PLUMED and was included by using a LOAD command More details ...
ARG=d1
NSTATES=2
FILENAME=gaussian
PACE=500
LABEL=ext
BIAS_CUTOFF
CUTOFF=100
LAMBDA=0.1
TEMPERATURE=300
... GAMBES

#..............................WALLS.................................................
uwall: UPPER_WALLS ARG=d1,d2,d3,d4,d5 AT=3.0,3.0,3.0,3.0,3.0 KAPPA=150.0,150.0,150.0,150.0,150.0  #eps=1, exp=2, offset=0 : defaultThis action is not part of PLUMED and was included by using a LOAD command More details values
H1: 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 details ATOMSthe numerical indexes for the set of atoms in the group=3,4
H2: 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 details ATOMSthe numerical indexes for the set of atoms in the group=7,8,9
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 details ATOMSthe numerical indexes for the set of atoms in the group=11
C_end: 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 details ATOMSthe numerical indexes for the set of atoms in the group=1,5
C_mid: 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 details ATOMSthe numerical indexes for the set of atoms in the group=2
Br: 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 details ATOMSthe numerical indexes for the set of atoms in the group=10
Ce1: 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 details ATOMSthe numerical indexes for the set of atoms in the group=1
Ce2: 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 details ATOMSthe numerical indexes for the set of atoms in the group=5
H_all: 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 details ATOMSthe numerical indexes for the set of atoms in the group=3,4,6,7,8,9,11
dCe1H1: DISTANCESCalculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Ce1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H1 HIGHESTthis flag allows you to recover the highest of these variables NOPBC ignore the periodic boundary conditions when calculating distances
dCe2H2: DISTANCESCalculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Ce2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H2 HIGHESTthis flag allows you to recover the highest of these variables NOPBC ignore the periodic boundary conditions when calculating distances
dCmH1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6 NOPBC ignore the periodic boundary conditions when calculating distances
dHH: DISTANCESCalculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H_all GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H_all MINcalculate the minimum value={BETA=20} NOPBC ignore the periodic boundary conditions when calculating distances
d13: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 NOPBC ignore the periodic boundary conditions when calculating distances
d14: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4 NOPBC ignore the periodic boundary conditions when calculating distances
wallCe1H1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe input for this action is the scalar output from one or more other actions=d13,d14 ATthe positions of the wall=1.4,1.4 KAPPAthe force constant for the wall=150.0,150.0 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2
d57: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7 NOPBC ignore the periodic boundary conditions when calculating distances
d58: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,8 NOPBC ignore the periodic boundary conditions when calculating distances
d59: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9 NOPBC ignore the periodic boundary conditions when calculating distances
wallCe2H2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe input for this action is the scalar output from one or more other actions=d57,d58,d59 ATthe positions of the wall=1.4,1.4,1.4 KAPPAthe force constant for the wall=150.0,150.0,150.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1.0,1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2,0.2
wallCmH1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe input for this action is the scalar output from one or more other actions=dCmH1 ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 OFFSET the offset for the start of the wall=0.2
wallHH: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe input for this action is the scalar output from one or more other actions=dHH ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 #OFFSET=1.3
##################################################

PRINTPrint quantities to a file. More details ARGthe input for this action is the scalar output from one or more other actions STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f
#PRINT ARG=ext.probability.0,ext.probability.1,ext.probability.2 STRIDE=10 FILE=GAMBES FMT=%8.10f
```