Project ID: plumID:19.074
Source: DNA-CGGC/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=120,121 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=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=52First list of atomsGROUPB=192Second 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=72First list of atomsGROUPB=172Second 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=93First list of atomsGROUPB=151Second 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=113First list of atomsGROUPB=131Second 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=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, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=31First list of atomsGROUPB=52Second 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=52First list of atomsGROUPB=72Second 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=72First list of atomsGROUPB=93Second 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=93First list of atomsGROUPB=113Second 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=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=213First list of atomsGROUPB=192Second 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=192First list of atomsGROUPB=172Second 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=172First list of atomsGROUPB=151Second 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=151First list of atomsGROUPB=131Second 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=-2.635specifies 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 120 121 #2 COORD LIST NN 6 MM 12 D_0 0.30 R_0 0.10 PAIR g1-> 235 232 g1<- g2-> 13 10 g2<- COORD LIST 31 213 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 52 192 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 72 172 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 93 151 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR COORD LIST 113 131 NN 6 MM 12 D_0 0.55 R_0 0.00001 PAIR # 3prime COORD LIST 11 31 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 31 52 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 52 72 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 72 93 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 93 113 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR # 5prime COORD LIST 233 213 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 213 192 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 192 172 NN 6 MM 12 D_0 0.80 R_0 0.00001 PAIR COORD LIST 172 151 NN 6 MM 12 D_0 0.75 R_0 0.00001 PAIR COORD LIST 151 131 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 -2.635 </span></pre>