Project ID: plumID:19.074
Source: DNA-CCGG/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=1-240 d:the atoms that make up a molecule that you wish to alignDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=111,112 co:the pair of atom that we are calculating the distance betweenCOORDINATIONCalculate coordination numbers. More detailsGROUPA=235,232First list of atomsGROUPB=13,10Second 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=30First list of atomsGROUPB=211Second 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=49First list of atomsGROUPB=189Second 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=68First list of atomsGROUPB=167Second 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=87First list of atomsGROUPB=145Second 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=106First list of atomsGROUPB=123Second 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=30First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=49First list of atomsGROUPB=30Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=68First list of atomsGROUPB=49Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=87First list of atomsGROUPB=68Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=106First list of atomsGROUPB=87Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=211First list of atomsGROUPB=233Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=189First list of atomsGROUPB=211Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=167First list of atomsGROUPB=189Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=145First list of atomsGROUPB=167Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=123First list of atomsGROUPB=145Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.70The 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=-2.606specifies 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 1 240 1 align<- #1 DISTANCE LIST 111 112 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 235 232 g1<- g2-> 13 10 g2<- #3 COORD LIST 30 211 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 49 189 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 68 167 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 87 145 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 106 123 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 30 11 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 49 30 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 68 49 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 87 68 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 106 87 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 211 233 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 189 211 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 167 189 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 145 167 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 123 145 NN 6 MM 12 D_0 0.70 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 -2.606 </span></pre>