Project ID: plumID:21.030
Source: plumed-nest/nspe/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#! vim:ft=plumed
#RESTART #DEBUG logActivity FILE=debug.dat
ene:ENERGYCalculate the total potential energy of the simulation box. More detailsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=cn.dat # The command: # INCLUDE FILE=cn.dat # ensures PLUMED loads the contents of the file called cn.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
# coordination r1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=13,22 #res 1 and 10 agg in trial 1 r2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=41,50 r3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=64,73 r4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=87,96 r5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=110,119 r6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=133,142 #res 6 and 9 should be coordinated in a helix r7:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=156,165 r8:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=179,188 r9:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=202,211 #CG-CH r10:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=225,234 r11:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=248,257 r12:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=270,279the list of atoms which are involved the virtual atom's definition
# coordination c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r2,r2,r2,r2,r2,r2,r2,r2,r2,r2,r3,r3,r3,r3,r3,r3,r3,r3,r3,r4,r4,r4,r4,r4,r4,r4,r4,r5,r5,r5,r5,r5,r5,r5,r6,r6,r6,r6,r6,r6,r7,r7,r7,r7,r7,r8,r8,r8,r8,r9,r9,r9,r10,r10,r11First list of atomsGROUPB=r2,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r4,r5,r6,r7,r8,r9,r10,r11,r12,r5,r6,r7,r8,r9,r10,r11,r12,r6,r7,r8,r9,r10,r11,r12,r7,r8,r9,r10,r11,r12,r8,r9,r10,r11,r12,r9,r10,r11,r12,r10,r11,r12,r11,r12,r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10The frequency with which we are updating the atoms in the neighbor listPAIRPair only 1st element of the 1st group with 1st element in the second, etc
# each ring coord The COORDINATION action with label c calculates a scalar quantityc1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c1 calculates a scalar quantityc2:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c2 calculates a scalar quantityc3:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c3 calculates a scalar quantityc4:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c4 calculates a scalar quantityc5:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c5 calculates a scalar quantityc6:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c6 calculates a scalar quantityc7:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c7 calculates a scalar quantityc8:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c8 calculates a scalar quantityc9:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c9 calculates a scalar quantityc10:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c10 calculates a scalar quantityc11:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c11 calculates a scalar quantityc12:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c12 calculates a scalar quantityc13:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c13 calculates a scalar quantityc14:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c14 calculates a scalar quantityc15:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c15 calculates a scalar quantityc16:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c16 calculates a scalar quantityc17:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c17 calculates a scalar quantityc18:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c18 calculates a scalar quantityc19:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c19 calculates a scalar quantityc20:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c20 calculates a scalar quantityc21:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c21 calculates a scalar quantityc22:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c22 calculates a scalar quantityc23:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c23 calculates a scalar quantityc24:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c24 calculates a scalar quantityc25:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c25 calculates a scalar quantityc26:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c26 calculates a scalar quantityc27:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c27 calculates a scalar quantityc28:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c28 calculates a scalar quantityc29:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c29 calculates a scalar quantityc30:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c30 calculates a scalar quantityc31:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c31 calculates a scalar quantityc32:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c32 calculates a scalar quantityc33:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c33 calculates a scalar quantityc34:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c34 calculates a scalar quantityc35:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c35 calculates a scalar quantityc36:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c36 calculates a scalar quantityc37:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c37 calculates a scalar quantityc38:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c38 calculates a scalar quantityc39:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c39 calculates a scalar quantityc40:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c40 calculates a scalar quantityc41:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c41 calculates a scalar quantityc42:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c42 calculates a scalar quantityc43:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c43 calculates a scalar quantityc44:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c44 calculates a scalar quantityc45:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c45 calculates a scalar quantityc46:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c46 calculates a scalar quantityc47:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c47 calculates a scalar quantityc48:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c48 calculates a scalar quantityc49:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c49 calculates a scalar quantityc50:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c50 calculates a scalar quantityc51:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c51 calculates a scalar quantityc52:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c52 calculates a scalar quantityc53:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c53 calculates a scalar quantityc54:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c54 calculates a scalar quantityc55:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c55 calculates a scalar quantityc56:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c56 calculates a scalar quantityc57:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c57 calculates a scalar quantityc58:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c58 calculates a scalar quantityc59:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c59 calculates a scalar quantityc60:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c60 calculates a scalar quantityc61:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c61 calculates a scalar quantityc62:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c62 calculates a scalar quantityc63:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c63 calculates a scalar quantityc64:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r10First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c64 calculates a scalar quantityc65:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r10First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c65 calculates a scalar quantityc66:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=r11First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10The frequency with which we are updating the atoms in the neighbor list
# --- End of included input --- The COORDINATION action with label c66 calculates a scalar quantityINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=cv.dat # The command: # INCLUDE FILE=cv.dat # ensures PLUMED loads the contents of the file called cv.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
#RESTART
# COLVARS
# rg rg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1,3,4,29,31,32,52,54,55,75,77,78,98,100,101,121,123,124,144,146,147,167,169,170,190,192,193,213,215,216,236,238,239,259,261the group of atoms that you are calculating the Gyration Tensor for
# dihedrals # phi phi0:TORSIONCalculate a torsional angle. More detailsATOMS=24,4,3,1 The TORSION action with label phi0 calculates a scalar quantityphi1:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=1,32,31,29 The TORSION action with label phi1 calculates a scalar quantityphi2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=29,55,54,52 The TORSION action with label phi2 calculates a scalar quantityphi3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=52,78,77,75 The TORSION action with label phi3 calculates a scalar quantityphi4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=75,101,100,98 The TORSION action with label phi4 calculates a scalar quantityphi5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=98,124,123,121 The TORSION action with label phi5 calculates a scalar quantityphi6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=121,147,146,144 The TORSION action with label phi6 calculates a scalar quantityphi7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=144,170,169,167 The TORSION action with label phi7 calculates a scalar quantityphi8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=167,193,192,190 The TORSION action with label phi8 calculates a scalar quantityphi9:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=190,216,215,213 The TORSION action with label phi9 calculates a scalar quantityphi10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=213,239,238,236the four atoms involved in the torsional angle
# psi The TORSION action with label phi10 calculates a scalar quantitypsi0:TORSIONCalculate a torsional angle. More detailsATOMS=26,24,4,3 The TORSION action with label psi0 calculates a scalar quantitypsi1:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=3,1,32,31 The TORSION action with label psi1 calculates a scalar quantitypsi2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=31,29,55,54 The TORSION action with label psi2 calculates a scalar quantitypsi3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=54,52,78,77 The TORSION action with label psi3 calculates a scalar quantitypsi4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=77,75,101,100 The TORSION action with label psi4 calculates a scalar quantitypsi5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=100,98,124,123 The TORSION action with label psi5 calculates a scalar quantitypsi6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=123,121,147,146 The TORSION action with label psi6 calculates a scalar quantitypsi7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=146,144,170,169 The TORSION action with label psi7 calculates a scalar quantitypsi8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=169,167,193,192 The TORSION action with label psi8 calculates a scalar quantitypsi9:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=192,190,216,215 The TORSION action with label psi9 calculates a scalar quantitypsi10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=215,213,239,238 The TORSION action with label psi10 calculates a scalar quantitypsi11:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=238,236,261,259the four atoms involved in the torsional angle
# omega The TORSION action with label psi11 calculates a scalar quantityomega0:TORSIONCalculate a torsional angle. More detailsATOMS=4,3,1,32 The TORSION action with label omega0 calculates a scalar quantityomega1:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=32,31,29,55 The TORSION action with label omega1 calculates a scalar quantityomega2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=55,54,52,78 The TORSION action with label omega2 calculates a scalar quantityomega3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=78,77,75,101 The TORSION action with label omega3 calculates a scalar quantityomega4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=101,100,98,124 The TORSION action with label omega4 calculates a scalar quantityomega5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=124,123,121,147 The TORSION action with label omega5 calculates a scalar quantityomega6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=147,146,144,170 The TORSION action with label omega6 calculates a scalar quantityomega7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=170,169,167,193 The TORSION action with label omega7 calculates a scalar quantityomega8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=193,192,190,216 The TORSION action with label omega8 calculates a scalar quantityomega9:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=216,215,213,239 The TORSION action with label omega9 calculates a scalar quantityomega10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=239,238,236,261the four atoms involved in the torsional angle
# chi-1 The TORSION action with label omega10 calculates a scalar quantitychi0:TORSIONCalculate a torsional angle. More detailsATOMS=4,3,7,9 The TORSION action with label chi0 calculates a scalar quantitychi1:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=32,31,35,37 The TORSION action with label chi1 calculates a scalar quantitychi2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=55,54,58,60 The TORSION action with label chi2 calculates a scalar quantitychi3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=78,77,81,83 The TORSION action with label chi3 calculates a scalar quantitychi4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=101,100,104,106 The TORSION action with label chi4 calculates a scalar quantitychi5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=124,123,127,129 The TORSION action with label chi5 calculates a scalar quantitychi6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=147,146,150,152 The TORSION action with label chi6 calculates a scalar quantitychi7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=170,169,173,175 The TORSION action with label chi7 calculates a scalar quantitychi8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=193,192,196,198 The TORSION action with label chi8 calculates a scalar quantitychi9:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=216,215,219,221 The TORSION action with label chi9 calculates a scalar quantitychi10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=239,238,242,244 The TORSION action with label chi10 calculates a scalar quantitychi11:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=261,259,264,266the four atoms involved in the torsional angle
# chi-2 The TORSION action with label chi11 calculates a scalar quantitychi20:TORSIONCalculate a torsional angle. More detailsATOMS=3,7,13,14 The TORSION action with label chi20 calculates a scalar quantitychi21:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=31,35,41,42 The TORSION action with label chi21 calculates a scalar quantitychi22:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=54,58,64,65 The TORSION action with label chi22 calculates a scalar quantitychi23:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=77,81,87,88 The TORSION action with label chi23 calculates a scalar quantitychi24:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=100,104,110,111 The TORSION action with label chi24 calculates a scalar quantitychi25:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=123,127,133,134 The TORSION action with label chi25 calculates a scalar quantitychi26:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=146,150,156,157 The TORSION action with label chi26 calculates a scalar quantitychi27:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=169,173,179,180 The TORSION action with label chi27 calculates a scalar quantitychi28:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=192,196,202,203 The TORSION action with label chi28 calculates a scalar quantitychi29:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=215,219,225,226 The TORSION action with label chi29 calculates a scalar quantitychi210:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=238,242,248,249 The TORSION action with label chi210 calculates a scalar quantitychi211:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=259,264,270,271the four atoms involved in the torsional angle
# --- End of included input --- The TORSION action with label chi211 calculates a scalar quantityINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=ab.dat # The command: # INCLUDE FILE=ab.dat # ensures PLUMED loads the contents of the file called ab.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
#alphaD- cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_d_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#alphaD- transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_d_minus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#alphaD+ cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_d_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#alphaD+ transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_d_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha+ cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha+ transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha- cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha- transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_minus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=c7beta_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=c7beta_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta- cisALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=c7beta_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ transALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=c7beta_minus_trans ... ALPHABETA # --- End of included input ---a label for the action so that its output can be referenced in the input to other actions
# WTEMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=enethe input for this action is the scalar output from one or more other actionsPACE=5000the frequency for hill additionBIASFACTOR=60.0use well tempered metadynamics and use this bias factorHEIGHT=2.0the heights of the Gaussian hillsSIGMA=150the widths of the Gaussian hillsGRID_MIN=-500000the lower bounds for the gridGRID_MAX=-100000the upper bounds for the gridFILE=../HILLS_enea file in which the list of added hills is storedLABEL=wtemetad ... METADa label for the action so that its output can be referenced in the input to other actions
The METAD action with label wtemetad calculates the following quantities:
Quantity Description wtemetad.bias the instantaneous value of the bias potential PBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=c,c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c18,c19,c20,c21,c22,c23,c24,c25,c26,c27,c28,c29,c30,c31,c32,c33,c34,c35,c36,c37,c38,c39,c40,c41,c42,c43,c44,c45,c46,c47,c48,c49,c50,c51,c52,c53,c54,c55,c56,c57,c58,c59,c60,c61,c62,c63,c64,c65,c66,rg,alpha_d_plus,alpha_d_minus,alpha_plus,alpha_minus,c7beta_plus,c7beta_minus,alpha_d_plus_trans,alpha_d_minus_trans,alpha_plus_trans,alpha_minus_trans,c7beta_plus_trans,c7beta_minus_trans,omega0,omega1,omega2,omega3,omega4,omega5,omega6,omega7,omega8,omega9,omega10,phi0,phi1,phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,psi0,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,chi0,chi1,chi2,chi3,chi4,chi5,chi6,chi7,chi8,chi9,chi10,chi11,chi20,chi21,chi22,chi23,chi24,chi25,chi26,chi27,chi28,chi29,chi210,chi211the input for this action is the scalar output from one or more other actionsSIGMA=0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.1,1,1,1,1,1,1,1,1,1,1,1,1,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35the widths of the Gaussian hillsHEIGHT=2.5 #kj/molthe height of the Gaussian hills, one for all biasesPACE=1000the frequency for hill addition, one for all biasesBIASFACTOR=140 #max rule baseBF x sqrt(NCV) ~ 100 (BF = ~12 for 10kcal/mol hill height cis/trans isom, CV=131) # TEMP=300use well tempered metadynamics with this bias factor, one for all biasesGRID_MIN=-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pithe lower bounds for the gridGRID_MAX=40,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,3,50,50,50,50,50,50,50,50,50,50,50,50,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pithe upper bounds for the gridLABEL=pba label for the action so that its output can be referenced in the input to other actionsFILE=../HILLS_cn,../HILLS_c1,../HILLS_c2,../HILLS_c3,../HILLS_c4,../HILLS_c5,../HILLS_c6,../HILLS_c7,../HILLS_c8,../HILLS_c9,../HILLS_c10,../HILLS_c11,../HILLS_c12,../HILLS_c13,../HILLS_c14,../HILLS_c15,../HILLS_c16,../HILLS_c17,../HILLS_c18,../HILLS_c19,../HILLS_c20,../HILLS_c21,../HILLS_c22,../HILLS_c23,../HILLS_c24,../HILLS_c25,../HILLS_c26,../HILLS_c27,../HILLS_c28,../HILLS_c29,../HILLS_c30,../HILLS_c31,../HILLS_c32,../HILLS_c33,../HILLS_c34,../HILLS_c35,../HILLS_c36,../HILLS_c37,../HILLS_c38,../HILLS_c39,../HILLS_c40,../HILLS_c41,../HILLS_c42,../HILLS_c43,../HILLS_c44,../HILLS_c45,../HILLS_c46,../HILLS_c47,../HILLS_c48,../HILLS_c49,../HILLS_c50,../HILLS_c51,../HILLS_c52,../HILLS_c53,../HILLS_c54,../HILLS_c55,../HILLS_c56,../HILLS_c57,../HILLS_c58,../HILLS_c59,../HILLS_c60,../HILLS_c61,../HILLS_c62,../HILLS_c63,../HILLS_c64,../HILLS_c65,../HILLS_c66,../HILLS_rg,../HILLS_alpha_d_plus,../HILLS_alpha_d_minus,../HILLS_alpha_plus,../HILLS_alpha_minus,../HILLS_c7beta_plus,../HILLS_c7beta_minus,../HILLS_alpha_d_plus_trans,../HILLS_alpha_d_minus_trans,../HILLS_alpha_plus_trans,../HILLS_alpha_minus_trans,../HILLS_c7beta_plus_trans,../HILLS_c7beta_minus_trans,../HILLS_omega0,../HILLS_omega1,../HILLS_omega2,../HILLS_omega3,../HILLS_omega4,../HILLS_omega5,../HILLS_omega6,../HILLS_omega7,../HILLS_omega8,../HILLS_omega9,../HILLS_omega10,../HILLS_phi0,../HILLS_phi1,../HILLS_phi2,../HILLS_phi3,../HILLS_phi4,../HILLS_phi5,../HILLS_phi6,../HILLS_phi7,../HILLS_phi8,../HILLS_phi9,../HILLS_phi10,../HILLS_psi0,../HILLS_psi1,../HILLS_psi2,../HILLS_psi3,../HILLS_psi4,../HILLS_psi5,../HILLS_psi6,../HILLS_psi7,../HILLS_psi8,../HILLS_psi9,../HILLS_psi10,../HILLS_psi11,../HILLS_chi0,../HILLS_chi1,../HILLS_chi2,../HILLS_chi3,../HILLS_chi4,../HILLS_chi5,../HILLS_chi6,../HILLS_chi7,../HILLS_chi8,../HILLS_chi9,../HILLS_chi10,../HILLS_chi11,../HILLS_chi20,../HILLS_chi21,../HILLS_chi22,../HILLS_chi23,../HILLS_chi24,../HILLS_chi25,../HILLS_chi26,../HILLS_chi27,../HILLS_chi28,../HILLS_chi29,../HILLS_chi210,../HILLS_chi211 ... PBMETADfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
The PBMETAD action with label pb calculates the following quantities:
Quantity Description pb.bias the instantaneous value of the bias potential Print quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities