PLUMED-NEST

Project ID: plumID:19.074
Source: RNA-UAAU/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

# 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
=1-246
d: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=123,124
The DISTANCE action with label d calculates a scalar quantityco: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=11,10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=239,238 
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
The COORDINATION action with label co calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=32 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=218 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=53 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=197 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=74 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=176 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=95 
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
=0.55 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=116 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=134 
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
The COORDINATION action with label  calculates a scalar quantity
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)
=32 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=32 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=53 
D_0
 The d_0 parameter of the switching function
=0.80 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=53 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=74 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=74 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=95 
D_0
 The d_0 parameter of the switching function
=0.80 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=95 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=116 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=239 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=218 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=218 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=197 
D_0
 The d_0 parameter of the switching function
=0.80 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=197 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=176 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=176 
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
=0.80 
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
The COORDINATION action with label  calculates a scalar quantity
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)
=134 
D_0
 The d_0 parameter of the switching function
=0.90 
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
The COORDINATION action with label  calculates a scalar quantity
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
=-2.635

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 1 246 1
align<-

#1
DISTANCE LIST 123 124

#2 
COORD LIST   NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR

g1->
11 10
g1<-

g2->
239 238 
g2<-

#3
COORD LIST 32 218 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 53 197 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 74 176 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 95 155 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 116 134 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR


#8 3prime strand in this pulling framework
COORD LIST 11 32 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 32 53 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 53 74 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 74 95 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 95 116 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR

#13 5prime strand in this pulling framework
COORD LIST 239 218 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 218 197 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 197 176 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 176 155 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 155 134 NN 6 MM 12 D_0 0.90 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 -2.635
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