Project ID: plumID:19.074
Source: DNA-CAGT/3G5C/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=111,110First list of atomsGROUPB=129,128Second 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=91First list of atomsGROUPB=149Second 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=71First list of atomsGROUPB=171Second 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=51First list of atomsGROUPB=191Second 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=31First list of atomsGROUPB=213Second 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=11First list of atomsGROUPB=233Second 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=149First list of atomsGROUPB=129Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=171First list of atomsGROUPB=149Second 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=191First list of atomsGROUPB=171Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=213First list of atomsGROUPB=191Second 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=233First list of atomsGROUPB=213Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=91First list of atomsGROUPB=111Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=71First list of atomsGROUPB=91Second 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=51First list of atomsGROUPB=71Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=31First list of atomsGROUPB=51Second 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=11First list of atomsGROUPB=31Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.80The 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=-2.60667specifies 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-> 111 110 g1<- g2-> 129 128 g2<- #3 COORD LIST 91 149 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 71 171 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 51 191 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 31 213 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 11 233 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 149 129 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 171 149 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 191 171 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 213 191 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 233 213 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 91 111 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 71 91 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 51 71 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 31 51 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 11 31 NN 6 MM 12 D_0 0.80 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 -2.60667 </span></pre>