Project ID: plumID:19.074
Source: RNA-AAUU/3A5U/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=1-246 d:the atoms that make up a molecule that you wish to alignDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=129,130 co:the pair of atom that we are calculating the distance betweenCOORDINATIONCalculate coordination numbers. More detailsGROUPA=11,12First list of atomsGROUPB=239,240Second 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=220First list of atomsGROUPB=34Second 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=200First list of atomsGROUPB=56Second 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=180First list of atomsGROUPB=78Second 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=160First list of atomsGROUPB=100Second 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=140First list of atomsGROUPB=122Second 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=34First 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, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=56First list of atomsGROUPB=34Second 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=78First list of atomsGROUPB=56Second 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=100First list of atomsGROUPB=78Second 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=122First list of atomsGROUPB=100Second 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=220First list of atomsGROUPB=240Second 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=200First list of atomsGROUPB=220Second 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=180First list of atomsGROUPB=200Second 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=160First list of atomsGROUPB=180Second 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=140First list of atomsGROUPB=160Second 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=-2.52167specifies 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 1 246 1 align<- #1 DISTANCE LIST 129 130 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 11 12 g1<- g2-> 239 240 g2<- #3 COORD LIST 220 34 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 200 56 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 180 78 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 160 100 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 140 122 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 34 12 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 56 34 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 78 56 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 100 78 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 122 100 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 220 240 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 200 220 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 180 200 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 160 180 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 140 160 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 -2.52167 </span></pre>