Project ID: plumID:19.074
Source: DNA-TAAT/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=114,113First list of atomsGROUPB=132,131Second 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=94First list of atomsGROUPB=152Second 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=73First list of atomsGROUPB=173Second 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=53First list of atomsGROUPB=193Second 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=32First list of atomsGROUPB=214Second 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=234Second 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=132First list of atomsGROUPB=152Second 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=152First list of atomsGROUPB=173Second 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=173First list of atomsGROUPB=193Second 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=193First list of atomsGROUPB=214Second 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=214First list of atomsGROUPB=234Second 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=114First list of atomsGROUPB=94Second 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=94First list of atomsGROUPB=73Second 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=73First list of atomsGROUPB=53Second 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=53First list of atomsGROUPB=32Second 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=32First list of atomsGROUPB=12Second 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=-2.52167specifies 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 1 240 1 align<- #1 DISTANCE LIST 1 240 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 114 113 g1<- g2-> 132 131 g2<- #3 COORD LIST 94 152 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 73 173 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 53 193 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 32 214 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 12 234 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR #8 3prime strand in this pulling framework COORD LIST 132 152 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 152 173 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 173 193 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 193 214 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 214 234 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR #13 5prime strand in this pulling framework COORD LIST 114 94 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 94 73 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 73 53 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 53 32 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 32 12 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 -2.52167 </span></pre>