PLUMED-NEST

Project ID: plumID:22.004
Source: input_files/Claisen_reaction/2_Sampling/plumed.dat
Originally used with PLUMED version: 2.8
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

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

a_1_2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_2 calculates a scalar quantitya_1_3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_3 calculates a scalar quantitya_1_4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=4 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_4 calculates a scalar quantitya_1_5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_5 calculates a scalar quantitya_1_6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
R_0
The r_0 parameter of the switching function
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_6 calculates a scalar quantitya_1_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_7 calculates a scalar quantitya_1_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_8 calculates a scalar quantitya_1_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_9 calculates a scalar quantitya_1_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_10 calculates a scalar quantitya_1_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_11 calculates a scalar quantitya_1_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_12 calculates a scalar quantitya_1_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_1_13 calculates a scalar quantitya_1_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_1_14 calculates a scalar quantitya_2_3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_3 calculates a scalar quantitya_2_4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=4 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_4 calculates a scalar quantitya_2_5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_5 calculates a scalar quantitya_2_6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_6 calculates a scalar quantitya_2_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_7 calculates a scalar quantitya_2_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_8 calculates a scalar quantitya_2_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_9 calculates a scalar quantitya_2_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_10 calculates a scalar quantitya_2_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_11 calculates a scalar quantitya_2_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_12 calculates a scalar quantitya_2_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_2_13 calculates a scalar quantitya_2_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_2_14 calculates a scalar quantitya_3_4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=4 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_4 calculates a scalar quantitya_3_5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_5 calculates a scalar quantitya_3_6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_6 calculates a scalar quantitya_3_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_7 calculates a scalar quantitya_3_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_8 calculates a scalar quantitya_3_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_9 calculates a scalar quantitya_3_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_10 calculates a scalar quantitya_3_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_11 calculates a scalar quantitya_3_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_12 calculates a scalar quantitya_3_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_3_13 calculates a scalar quantitya_3_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_3_14 calculates a scalar quantitya_4_5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_5 calculates a scalar quantitya_4_6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
R_0
The r_0 parameter of the switching function
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_6 calculates a scalar quantitya_4_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_7 calculates a scalar quantitya_4_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_8 calculates a scalar quantitya_4_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_9 calculates a scalar quantitya_4_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_10 calculates a scalar quantitya_4_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_11 calculates a scalar quantitya_4_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_12 calculates a scalar quantitya_4_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_4_13 calculates a scalar quantitya_4_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_4_14 calculates a scalar quantitya_5_6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=6 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_6 calculates a scalar quantitya_5_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_7 calculates a scalar quantitya_5_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_8 calculates a scalar quantitya_5_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_9 calculates a scalar quantitya_5_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_10 calculates a scalar quantitya_5_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_11 calculates a scalar quantitya_5_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_12 calculates a scalar quantitya_5_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_5_13 calculates a scalar quantitya_5_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_5_14 calculates a scalar quantitya_6_7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7 
R_0
The r_0 parameter of the switching function
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_7 calculates a scalar quantitya_6_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_8 calculates a scalar quantitya_6_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_9 calculates a scalar quantitya_6_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_10 calculates a scalar quantitya_6_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_11 calculates a scalar quantitya_6_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_12 calculates a scalar quantitya_6_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_6_13 calculates a scalar quantitya_6_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_6_14 calculates a scalar quantitya_7_8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=8 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_8 calculates a scalar quantitya_7_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_9 calculates a scalar quantitya_7_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_10 calculates a scalar quantitya_7_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_11 calculates a scalar quantitya_7_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_12 calculates a scalar quantitya_7_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_7_13 calculates a scalar quantitya_7_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_7_14 calculates a scalar quantitya_8_9: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=9 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_8_9 calculates a scalar quantitya_8_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_8_10 calculates a scalar quantitya_8_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_8_11 calculates a scalar quantitya_8_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_8_12 calculates a scalar quantitya_8_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_8_13 calculates a scalar quantitya_8_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_8_14 calculates a scalar quantitya_9_10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_9_10 calculates a scalar quantitya_9_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_9_11 calculates a scalar quantitya_9_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_9_12 calculates a scalar quantitya_9_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_9_13 calculates a scalar quantitya_9_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_9_14 calculates a scalar quantitya_10_11: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=11 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_10_11 calculates a scalar quantitya_10_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_10_12 calculates a scalar quantitya_10_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_10_13 calculates a scalar quantitya_10_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_10_14 calculates a scalar quantitya_11_12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=11 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_11_12 calculates a scalar quantitya_11_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=11 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_11_13 calculates a scalar quantitya_11_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=11 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_11_14 calculates a scalar quantitya_12_13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=12 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=13 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	
The COORDINATION action with label a_12_13 calculates a scalar quantitya_12_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=12 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	

The COORDINATION action with label a_12_14 calculates a scalar quantitya_13_14: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=13 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=14 
R_0
The r_0 parameter of the switching function
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=8	


The COORDINATION action with label a_13_14 calculates a scalar quantitycv: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=torch_cv.pt 
ARG
the input for this action is the scalar output from one or more other actions
=a_1_2,a_1_3,a_1_4,a_1_5,a_1_6,a_1_7,a_1_8,a_1_9,a_1_10,a_1_11,a_1_12,a_1_13,a_1_14,a_2_3,a_2_4,a_2_5,a_2_6,a_2_7,a_2_8,a_2_9,a_2_10,a_2_11,a_2_12,a_2_13,a_2_14,a_3_4,a_3_5,a_3_6,a_3_7,a_3_8,a_3_9,a_3_10,a_3_11,a_3_12,a_3_13,a_3_14,a_4_5,a_4_6,a_4_7,a_4_8,a_4_9,a_4_10,a_4_11,a_4_12,a_4_13,a_4_14,a_5_6,a_5_7,a_5_8,a_5_9,a_5_10,a_5_11,a_5_12,a_5_13,a_5_14,a_6_7,a_6_8,a_6_9,a_6_10,a_6_11,a_6_12,a_6_13,a_6_14,a_7_8,a_7_9,a_7_10,a_7_11,a_7_12,a_7_13,a_7_14,a_8_9,a_8_10,a_8_11,a_8_12,a_8_13,a_8_14,a_9_10,a_9_11,a_9_12,a_9_13,a_9_14,a_10_11,a_10_12,a_10_13,a_10_14,a_11_12,a_11_13,a_11_14,a_12_13,a_12_14,a_13_14   

The PYTORCH_MODEL action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.node
Model outputscv2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=cv 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO  

uw: 
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
=cv2 
AT
the positions of the wall
=3.0 
KAPPA
the force constant for the wall
=1000
lw: 
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
=cv2 
AT
the positions of the wall
=-3.0 
KAPPA
the force constant for the wall
=1000

opes: 
OPES_METAD_EXPLORE
On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details
 ... 
  
ARG
the input for this action is the scalar output from one or more other actions
=cv2
  
PACE
the frequency for kernel deposition
=1000
  
BARRIER
the free energy barrier to be overcome
=250
  
TEMP
 temperature
=300.0
...

The OPES_METAD_EXPLORE action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cv2.*,opes.*,uw.bias,lw.bias 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=20