PLUMED-NEST

Project ID: plumID:19.074
Source: RNA-UAAU/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=1-246
The WHOLEMOLECULES action with label  calculates somethingdThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,124
coThe COORDINATION action with label co calculates the following quantities:
 Quantity   
 Type   
 Description  
co
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=11,10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=239,238 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
co: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=11,10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=239,238 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  NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=32 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=218 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=53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=197 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=74 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=176 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=95 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=0.55 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=116 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=0.55 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=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
COORDINATIONCalculate 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
COORDINATIONCalculate 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
COORDINATIONCalculate 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
COORDINATIONCalculate 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=239 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=218 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=218 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=197 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=197 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=176 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
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=176 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
COORDINATIONCalculate 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
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=-2.635

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 1 246 1
align<-

#1
DISTANCE LIST 123 124

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

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