Project ID: plumID:19.074
Source: RNA-GACU/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
# vim:ft=plumed# plumed 2 syntax here, automatically translated from the original input fileEnables syntax highlighting for PLUMED files in vim. See here for more details.WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-249 d:the atoms that make up a molecule that you wish to alignDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,249 co:the pair of atom that we are calculating the distance betweenCOORDINATIONCalculate coordination numbers. More detailsGROUPA=143,142First list of atomsGROUPB=125,124Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.30The d_0 parameter of the switching functionR_0=0.10The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=102First list of atomsGROUPB=163Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.55The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=80First list of atomsGROUPB=183Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.55The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=57First list of atomsGROUPB=203Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.55The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=35First list of atomsGROUPB=223Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.55The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=12First list of atomsGROUPB=243Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.55The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=143First list of atomsGROUPB=163Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=163First list of atomsGROUPB=183Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=183First list of atomsGROUPB=203Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=203First list of atomsGROUPB=223Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=223First list of atomsGROUPB=243Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=125First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=102First list of atomsGROUPB=80Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=80First list of atomsGROUPB=57Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=57First list of atomsGROUPB=35Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=35First list of atomsGROUPB=12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.75The d_0 parameter of the switching functionR_0=0.00001The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cothe arguments on which the bias is actingAT=2the positions of the wallKAPPA=500the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=dthe arguments on which the bias is actingKAPPA=0specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=1.67the position of the restraintSLOPE=-2.57833specifies that the restraint is linear and what the values of the force constants on each of the variables areENDPLUMED# original input file with plumed 1.3 syntax follows PTMETAD PRINT W_STRIDE 500 ALIGN_ATOMS LISTTerminate plumed input. More detailsalign-> 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-> 143 142 g1<- g2-> 125 124 g2<- #3 COORD LIST 102 163 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 80 183 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 57 203 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 35 223 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 12 243 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 143 163 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 163 183 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 183 203 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 203 223 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 223 243 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 125 102 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 102 80 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 80 57 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 57 35 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 35 12 NN 6 MM 12 D_0 0.75 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 -2.57833 </span></pre>