Project ID: plumID:19.074
Source: DNA-GACT/3A5T/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 onv2.10
tested onmaster
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# plumed 2 syntax here, automatically translated from the original input file

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-240
d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=126,127
co: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=235,234 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=12,11 D_0 The d_0 parameter of the switching function=0.30 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=12 GROUPBSecond 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=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=34 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=216 D_0 The d_0 parameter of the switching function=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=55 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=196 D_0 The d_0 parameter of the switching function=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=77 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=177 D_0 The d_0 parameter of the switching function=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=98 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=157 D_0 The d_0 parameter of the switching function=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=138 D_0 The d_0 parameter of the switching function=0.55 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=34 GROUPBSecond 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_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=55 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=34 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=77 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=55 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=98 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=77 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=98 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=216 GROUPBSecond 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_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=196 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=216 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=177 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=196 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=157 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=177 D_0 The d_0 parameter of the switching function=0.70 R_0The 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=138 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=157 D_0 The d_0 parameter of the switching function=0.70 R_0The 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=co ATthe positions of the wall=2 KAPPAthe 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
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=d KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=0 ATthe 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=-2.55

ENDPLUMEDTerminate plumed input. More details

# original input file with plumed 1.3 syntax follows

PTMETAD
PRINT W_STRIDE 500
ALIGN_ATOMS LIST <align>
align->
LOOP 1 240 1
align<-

#1
DISTANCE LIST 126 127

#2 
COORD LIST <g1> <g2> NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR

g1->
235 234
g1<-

g2->
12 11 
g2<-

#3
COORD LIST 12 235 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 34 216 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 55 196 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 77 177 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 98 157 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 120 138 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR

#8 3prime strand in this pulling framework
COORD LIST 34 12 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 55 34 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 77 55 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 98 77 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 120 98 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR

#13 5prime strand in this pulling framework
COORD LIST 216 235 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 196 216 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 177 196 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 157 177 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 138 157 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 -2.55