PLUMED-NEST

Project ID: plumID:21.028
Source: hBromination/unbiased/anti_markovnikov/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=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

#UNITS
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

#LOAD FILES
The UNITS action with label  calculates something
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
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 distances 
d1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,11 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,1 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,1 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# ========= walls definition =========
# prevent hydrogen molecules 
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsH: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=3,4,6,7,8,9,11
The GROUP action with label H calculates somethingdHH: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H 
MIN
calculate the minimum value
={BETA=20} 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum colvarwallHH: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dHH 
AT
the positions of the wall
=1.4 
KAPPA
the 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

# keep COMs near
The LOWER_WALLS action with label wallHH calculates the following quantities:
 Quantity   
 Description  
wallHH.bias
the instantaneous value of the bias potential
wallHH.force2
the instantaneous value of the squared force due to this bias potentialuwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1,d2,d3,d4,d5 
AT
the positions of the wall
=3.0,3.0,3.0,3.0,3.0 
KAPPA
the force constant for the wall
=150.0,150.0,150.0,150.0,150.0 

# fix hydrogens on C1 -> bonding Br lateral
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentiald13: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,3 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,4 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomswallCe1H1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d13,d14 
AT
the positions of the wall
=1.4,1.4 
KAPPA
the 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

# fix hydrogens on C3 -> nonbonding Br lateral
The UPPER_WALLS action with label wallCe1H1 calculates the following quantities:
 Quantity   
 Description  
wallCe1H1.bias
the instantaneous value of the bias potential
wallCe1H1.force2
the instantaneous value of the squared force due to this bias potentiald57: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d57 calculates the following quantities:
 Quantity   
 Description  
d57.value
the DISTANCE between this pair of atomsd58: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,8 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d58 calculates the following quantities:
 Quantity   
 Description  
d58.value
the DISTANCE between this pair of atomsd59: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d59 calculates the following quantities:
 Quantity   
 Description  
d59.value
the DISTANCE between this pair of atomswallCe2H2: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d57,d58,d59 
AT
the positions of the wall
=1.4,1.4,1.4 
KAPPA
the 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

# fix hydrogen on C2 -> bonding Br central
The UPPER_WALLS action with label wallCe2H2 calculates the following quantities:
 Quantity   
 Description  
wallCe2H2.bias
the instantaneous value of the bias potential
wallCe2H2.force2
the instantaneous value of the squared force due to this bias potentiald26: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,6 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Description  
d26.value
the DISTANCE between this pair of atomswallCmH1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d26 
AT
the positions of the wall
=1.4 
KAPPA
the 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

# ====== CONTACTS =======
#DEFINE GROUP OF ATOMS
The UPPER_WALLS action with label wallCmH1 calculates the following quantities:
 Quantity   
 Description  
wallCmH1.bias
the instantaneous value of the bias potential
wallCmH1.force2
the instantaneous value of the squared force due to this bias potentialC: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1,2,5
#H: GROUP ATOMS=3,4,6,7,8,9,11
The GROUP action with label C calculates somethingBr: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=10

The GROUP action with label Br calculates somethingcc2: 
CONTACTS
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUPA=C SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
cb2: 
CONTACTS
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUPA=C GROUPB=Br SWITCH={RATIONAL D_0=0.0 R_0=1.9 NN=6 MM=8}
ch2: 
CONTACTS
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUPA=C GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
bh2: 
CONTACTS
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUPA=Br GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}

# ====== OUTPUT ======
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=50 
FILE
the name of the file on which to output these quantities
=distances 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=50 
FILE
the name of the file on which to output these quantities
=contacts 
ARG
the input for this action is the scalar output from one or more other actions
=cc2.*,cb2.*,ch2.*,bh2