Project ID: plumID:22.004
Source: input_files/Aldol_reaction/1_Discovery/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
tested onv2.10
tested onmaster
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A
a_1_1: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1 
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
=10	
a_1_2: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_3: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_4: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_5: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_1_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_1_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_1_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_1_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	

a_2_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_2 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_2_2: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=2 
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
=10	
a_2_3: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_4: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_5: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_2_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_3_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_3 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_3_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_3 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_3_3: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=3 
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
=10	
a_3_4: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_5: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_3_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_4_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_4 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_4_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_4 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_4_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_4 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_4_4: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=4 
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
=10	
a_4_5: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_4_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_4_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_4_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_4_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_4_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_4_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	

a_5_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_5 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_5_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_5 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_5_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_5 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_5_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_5 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_5_5: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=5 
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
=10	
a_5_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_5_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_5_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_5_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_5_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_5_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_6_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_6 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_6_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_6 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_6_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_6 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_6_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_6 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_6_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_6 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_6_6: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=6 
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
=10	
a_6_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_6_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_6_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_6_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_6_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	

a_7_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_6_7 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_7_7: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=7 
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
=10	
a_7_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_7_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_7_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.2 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_7_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_8_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_6_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_7: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_7_8 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_8_8: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=8 
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
=1.7 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	
a_8_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_8_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_8_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	

a_9_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_6_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_7: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_7_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_8: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_8_9 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_9_9: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=9 
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
=10	
a_9_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	
a_9_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_10_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_6_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_7: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_7_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_8: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_8_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_9: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_9_10 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_10_10: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=10 
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
=10	
a_10_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
=10	

a_11_1: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_1_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_2_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_3: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_3_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_4: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_4_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_5: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_5_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_6: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_6_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_7: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_7_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_8: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_8_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_9: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_9_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_10: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=a_10_11 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO	
a_11_11: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=11 
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
=1.6 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10	

cv: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=11_cv.pt 
ARG
the labels of the values from which the function is calculated
=a_1_1,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_2_1,a_2_2,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_3_1,a_3_2,a_3_3,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_4_1,a_4_2,a_4_3,a_4_4,a_4_5,a_4_6,a_4_7,a_4_8,a_4_9,a_4_10,a_4_11,a_5_1,a_5_2,a_5_3,a_5_4,a_5_5,a_5_6,a_5_7,a_5_8,a_5_9,a_5_10,a_5_11,a_6_1,a_6_2,a_6_3,a_6_4,a_6_5,a_6_6,a_6_7,a_6_8,a_6_9,a_6_10,a_6_11,a_7_1,a_7_2,a_7_3,a_7_4,a_7_5,a_7_6,a_7_7,a_7_8,a_7_9,a_7_10,a_7_11,a_8_1,a_8_2,a_8_3,a_8_4,a_8_5,a_8_6,a_8_7,a_8_8,a_8_9,a_8_10,a_8_11,a_9_1,a_9_2,a_9_3,a_9_4,a_9_5,a_9_6,a_9_7,a_9_8,a_9_9,a_9_10,a_9_11,a_10_1,a_10_2,a_10_3,a_10_4,a_10_5,a_10_6,a_10_7,a_10_8,a_10_9,a_10_10,a_10_11,a_11_1,a_11_2,a_11_3,a_11_4,a_11_5,a_11_6,a_11_7,a_11_8,a_11_9,a_11_10,a_11_11


#DEFINE WALLS WALLS
com1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-7
com2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=8-11

dc1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com2 
NOPBC
 ignore the periodic boundary conditions when calculating distances


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
=dc1  
AT
the positions of the wall
=+5.0 
KAPPA
the force constant for the wall
=150.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_1

opes: 
OPES_METAD_EXPLORE
On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=cv
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=200
  
TEMP
 temperature
=300.0
...

PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=cv.*,opes.*,*.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