Project ID: plumID:19.074
Source: DNA-AATT/3T5A/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
=1-240 d:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,240 co:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=117,116
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=135,134
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
=155
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=96
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
=175
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=75
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
=195
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=54
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
=215
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=33
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
=235
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
=0.55
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
=135
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=155
D_0
The d_0 parameter of the switching function
=0.70
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
=155
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=175
D_0
The d_0 parameter of the switching function
=0.70
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
=175
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=195
D_0
The d_0 parameter of the switching function
=0.70
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
=195
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=215
D_0
The d_0 parameter of the switching function
=0.70
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
=215
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=235
D_0
The d_0 parameter of the switching function
=0.70
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
=117
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=96
D_0
The d_0 parameter of the switching function
=0.70
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
=96
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=75
D_0
The d_0 parameter of the switching function
=0.70
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
=75
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=54
D_0
The d_0 parameter of the switching function
=0.70
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
=54
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=33
D_0
The d_0 parameter of the switching function
=0.70
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
=33
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
=0.70
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
=-2.40833
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 1 240 1 align<- #1 DISTANCE LIST 1 240 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 117 116 g1<- g2-> 135 134 g2<- #3 COORD LIST 155 96 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 175 75 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 195 54 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 215 33 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 235 12 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 135 155 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 155 175 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 175 195 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 195 215 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 215 235 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 117 96 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 96 75 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 75 54 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 54 33 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 33 12 NN 6 MM 12 D_0 0.70 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 -2.40833 </span></pre>