Project ID: plumID:19.074
Source: DNA-CCGG/3C5G/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=111,112
co: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=235,232 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=13,10 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=30 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=211 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=49 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=189 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=68 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=167 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=87 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=145 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=106 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 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=30 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=11 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=49 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=30 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=68 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=49 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=87 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=68 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=106 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=87 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=211 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=233 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=189 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=211 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=167 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=189 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=145 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=167 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=123 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=145 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=-2.606

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 111 112

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

g1->
235 232
g1<-

g2->
13 10
g2<-

#3
COORD LIST 30 211 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 49 189 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 68 167 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 87 145 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 106 123 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR

#8 3prime strand in this pulling framework
COORD LIST 30 11 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 49 30 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 68 49 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 87 68 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 106 87 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR

#13 5prime strand in this pulling framework
COORD LIST 211 233 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 189 211 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 167 189 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 145 167 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR
COORD LIST 123 145 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 -2.606