Project ID: plumID:19.074
Source: RNA-GACU/3C5G/plumed.dat
Originally used with PLUMED version: 2.5
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 onv2.9
tested onmaster
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.
# plumed 2 syntax here, automatically translated from the original input file
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=1-249 d:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,249 co:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=143,142
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=125,124
D_0
The d_0 parameter of the switching function
=0.30
R_0
The r_0 parameter of the switching function
=0.10
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=102
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=163
D_0
The d_0 parameter of the switching function
=0.55
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=80
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=183
D_0
The d_0 parameter of the switching function
=0.55
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=57
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=203
D_0
The d_0 parameter of the switching function
=0.55
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=35
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=223
D_0
The d_0 parameter of the switching function
=0.55
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
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)
=243
D_0
The d_0 parameter of the switching function
=0.55
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=143
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=163
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=163
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=183
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=183
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=203
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=203
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=223
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=223
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=243
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=125
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=102
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=102
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=80
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=80
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=57
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=57
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=35
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=35
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=12
D_0
The d_0 parameter of the switching function
=0.75
R_0
The r_0 parameter of the switching function
=0.00001
PAIR
Pair only 1st element of the 1st group with 1st element in the second, etc
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
=co
AT
the positions of the wall
=2
KAPPA
the force constant for the wall
=500
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=d
KAPPA
specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=0
AT
the position of the restraint
=1.67
SLOPE
specifies that the restraint is linear and what the values of the force constants on each of the variables are
=-2.57833
ENDPLUMED
Terminate plumed input. More details
# original input file with plumed 1.3 syntax follows PTMETAD PRINT W_STRIDE 500 ALIGN_ATOMS LIST align-> LOOP 1 249 1 align<- #1 DISTANCE LIST 1 249 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 143 142 g1<- g2-> 125 124 g2<- #3 COORD LIST 102 163 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 80 183 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 57 203 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 35 223 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 12 243 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 143 163 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 163 183 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 183 203 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 203 223 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 223 243 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 125 102 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 102 80 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 80 57 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 57 35 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 35 12 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR LWALL LIMIT 2 KAPPA 500.0 EXP 2.0 EPS 1.0 OFF 0.0 CV 2 UMBRELLA CV 1 KAPPA 0 AT 1.67 SLOPE -2.57833 </span></pre>