Project ID: plumID:19.074
Source: RNA-CGGC/plumed.dat
Originally used with PLUMED version: 2.5
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# vim:ft=plumed
# plumed 2 syntax here, automatically translated from the original input file

WHOLEMOLECULES ENTITY0=1-252
d: DISTANCE ATOMS=126,127
co: COORDINATION GROUPA=246,243 GROUPB=13,10 D_0=0.30 R_0=0.10 PAIR
COORDINATION GROUPA=32 GROUPB=223 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=54 GROUPB=201 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=75 GROUPB=180 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=97 GROUPB=158 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=118 GROUPB=137 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=11 GROUPB=32 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=32 GROUPB=54 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=54 GROUPB=75 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=75 GROUPB=97 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=97 GROUPB=118 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=244 GROUPB=223 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=223 GROUPB=201 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=201 GROUPB=180 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=180 GROUPB=158 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=158 GROUPB=137 D_0=0.90 R_0=0.00001 PAIR
LOWER_WALLS ARG=co AT=2 KAPPA=500 EXP=2 EPS=1
RESTRAINT ARG=d KAPPA=0 AT=1.67 SLOPE=-2.91833

ENDPLUMED

# original input file with plumed 1.3 syntax follows

PTMETAD
PRINT W_STRIDE 500
ALIGN_ATOMS LIST </span>
align->
LOOP 1 252 1
align<-

#1
DISTANCE LIST 126 127

#2
COORD LIST   NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR</span>

g1->
246 243
g1<-

g2->
13 10
g2<-

#3
COORD LIST 32 223 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 54 201 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 75 180 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 97 158 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 118 137 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR

#8 3prime
COORD LIST 11 32 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 32 54 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 54 75 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 75 97 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 97 118 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR

#13 5prime
COORD LIST 244 223 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 223 201 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 201 180 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 180 158 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 158 137 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 -2.91833


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