Project ID: plumID:19.074
Source: RNA-UAAU/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=1-246
d: DISTANCE ATOMS=123,124
co: COORDINATION GROUPA=11,10 GROUPB=239,238 D_0=0.30 R_0=0.10 PAIR
COORDINATION GROUPA=32 GROUPB=218 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=53 GROUPB=197 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=74 GROUPB=176 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=95 GROUPB=155 D_0=0.55 R_0=0.00001 PAIR
COORDINATION GROUPA=116 GROUPB=134 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=53 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=53 GROUPB=74 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=74 GROUPB=95 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=95 GROUPB=116 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=239 GROUPB=218 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=218 GROUPB=197 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=197 GROUPB=176 D_0=0.90 R_0=0.00001 PAIR
COORDINATION GROUPA=176 GROUPB=155 D_0=0.80 R_0=0.00001 PAIR
COORDINATION GROUPA=155 GROUPB=134 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=-2.635

ENDPLUMED

# original input file with plumed 1.3 syntax follows

PTMETAD
PRINT W_STRIDE 500
ALIGN_ATOMS LIST </span>
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</span>

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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