Project ID: plumID:19.074
Source: DNA-GACT/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=1,240 co:the pair of atom that we are calculating the distance betweenCOORDINATIONCalculate coordination numbers. More detailsGROUPA=120,119First list of atomsGROUPB=138,137Second 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=98First list of atomsGROUPB=157Second 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=77First list of atomsGROUPB=177Second 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=55First list of atomsGROUPB=196Second 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=216Second 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=235Second 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=138First list of atomsGROUPB=157Second 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=157First list of atomsGROUPB=177Second 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=177First list of atomsGROUPB=196Second 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=196First list of atomsGROUPB=216Second 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=216First 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=120First list of atomsGROUPB=98Second 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=98First list of atomsGROUPB=77Second 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=77First list of atomsGROUPB=55Second 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=55First list of atomsGROUPB=34Second 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=34First 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=-2.55specifies 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-> 120 119 g1<- g2-> 138 137 g2<- #3 COORD LIST 98 157 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 77 177 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 55 196 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 34 216 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 12 235 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 138 157 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 157 177 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 177 196 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 196 216 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 216 235 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 120 98 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 98 77 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 77 55 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 55 34 NN 6 MM 12 D_0 0.70 R_0 0.00001 PAIR COORD LIST 34 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 -2.55 </span></pre>