Project ID: plumID:19.074
Source: DNA-AATT/3T5A/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=1,240 co:the pair of atom that we are calculating the distance betweenCOORDINATIONCalculate coordination numbers. More detailsGROUPA=117,116First list of atomsGROUPB=135,134Second 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=155First list of atomsGROUPB=96Second 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=175First list of atomsGROUPB=75Second 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=195First list of atomsGROUPB=54Second 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=215First list of atomsGROUPB=33Second 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=235First list of atomsGROUPB=12Second 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=135First list of atomsGROUPB=155Second 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=155First list of atomsGROUPB=175Second 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=175First list of atomsGROUPB=195Second 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=195First list of atomsGROUPB=215Second 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=215First list of atomsGROUPB=235Second 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=117First list of atomsGROUPB=96Second 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=96First list of atomsGROUPB=75Second 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=75First list of atomsGROUPB=54Second 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=54First list of atomsGROUPB=33Second 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=33First list of atomsGROUPB=12Second 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=-2.40833specifies 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 1 240 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 117 116 g1<- g2-> 135 134 g2<- #3 COORD LIST 155 96 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 175 75 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 195 54 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 215 33 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 235 12 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 135 155 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 155 175 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 175 195 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 195 215 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 215 235 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 117 96 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 96 75 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 75 54 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 54 33 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 33 12 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 -2.40833 </span></pre>