PLUMED-NEST

Project ID: plumID:19.074
Source: RNA-CGGC/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=1-252
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=126,127
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=246,243 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
co: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=246,243 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  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)=223 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=54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=201 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=75 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=180 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=97 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=158 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=118 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=137 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)=54 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=54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=75 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=75 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=97 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=97 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=118 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=244 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=223 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=223 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=201 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=201 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=180 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=180 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=158 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=158 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=137 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=-2.91833

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 1 252 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->
246 243
g1<-

g2->
13 10
g2<-

#3
COORD LIST 32 223 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 54 201 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 75 180 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 97 158 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR
COORD LIST 118 137 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR

#8 3prime
COORD LIST 11 32 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 32 54 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 54 75 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 75 97 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 97 118 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR

#13 5prime
COORD LIST 244 223 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 223 201 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 201 180 NN 6 MM 12 D_0 0.90 R_0 0.00001 PAIR
COORD LIST 180 158 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR
COORD LIST 158 137 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 -2.91833