PLUMED-NEST by plumed-nest

Project ID: plumID:19.074
Source: RNA-CAGU/3G5C/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=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=1-249
d: DISTANCECalculate the distance between a pair of atoms. More details
 ATOMSthe pair of atom that we are calculating the distance between=1,249
The DISTANCE action with label d calculates a scalar quantityco: COORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=134,133 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=116,115 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
The COORDINATION action with label co calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=155 GROUPBSecond 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
=0.55 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=177 GROUPBSecond 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
=0.55 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=198 GROUPBSecond 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
=0.55 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=220 GROUPBSecond 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
=0.55 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=241 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
=0.55 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=155 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=177 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=198 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
=0.90 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=220 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=198 D_0 The d_0 parameter of the switching function
=0.80 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=241 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=220 D_0 The d_0 parameter of the switching function
=0.90 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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=95 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=74 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=53 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=32 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityCOORDINATIONCalculate coordination numbers. More details
 GROUPAFirst list of atoms
=11 GROUPBSecond 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_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
The COORDINATION action with label  calculates a scalar quantityLOWER_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 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 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=-2.66333

ENDPLUMEDTerminate plumed input. More details


# original input file with plumed 1.3 syntax follows

PTMETAD
PRINT W_STRIDE 500
ALIGN_ATOMS LIST 
align->
LOOP 1 249 1
align<-

#1
DISTANCE LIST 1 249

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

g1->
134 133
g1<-

g2->
116 115
g2<-

#3
COORD LIST 155 95 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 177 74 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 198 53 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 220 32 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 241 11 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR

#8 3prime strand in this pulling framework
COORD LIST 155 134 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 177 155 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 198 177 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 220 198 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 241 220 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR

#13 5prime strand in this pulling framework
COORD LIST 95 116 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 53 74 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 11 32 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 -2.66333
</span></pre>
PLUMED-NEST

The public repository of the PLUMED consortium
