**Project ID:** plumID:24.003

**Source:** plumed_nest/diff_helices/CH30-+/plumed.dat

**Originally used with PLUMED version:** 2.8-mod

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

#! vim:ft=plumed ## RESTARTWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-826the atoms that make up a molecule that you wish to align

# CHAIN ONE AND RESIDUE BEFORE LINKER The WHOLEMOLECULES action with label calculates somethingCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-399the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsp1The COM action with labelp1calculates the following quantities:

QuantityTypeDescriptionp1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=1-30the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsr1The COM action with labelr1calculates the following quantities:

QuantityTypeDescriptionr1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=376-399the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsr14The COM action with labelr14calculates the following quantities:

QuantityTypeDescriptionr14 atoms virtual atom calculated by COM action

# CHAIN TWO AND RESIDUE AFTER LINKERCOMCalculate the center of mass for a group of atoms. More detailsATOMS=434-826the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsp2The COM action with labelp2calculates the following quantities:

QuantityTypeDescriptionp2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=434-458the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsr16The COM action with labelr16calculates the following quantities:

QuantityTypeDescriptionr16 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=804-826the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsr30The COM action with labelr30calculates the following quantities:

QuantityTypeDescriptionr30 atoms virtual atom calculated by COM action DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp1,p2LABEL=a label for the action so that its output can be referenced in the input to other actionsdThe DISTANCE action with labeldcalculates the following quantities:

QuantityTypeDescriptiond scalar the DISTANCE between this pair of atoms DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenr14,r16LABEL=a label for the action so that its output can be referenced in the input to other actionsinThe DISTANCE action with labelincalculates the following quantities:

QuantityTypeDescriptionin scalar the DISTANCE between this pair of atoms DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenr1,r30LABEL=a label for the action so that its output can be referenced in the input to other actionsFRETThe DISTANCE action with labelFRETcalculates the following quantities:

QuantityTypeDescriptionFRET scalar the DISTANCE between this pair of atoms 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=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376,434,459,492,516,540,573,598,624,653,677,701,724,749,775,804the group of atoms that you are calculating the Gyration Tensor forLABEL=a label for the action so that its output can be referenced in the input to other actionsrgThe GYRATION action with labelrgcalculates the following quantities:

QuantityTypeDescriptionrg scalar the radius of gyration 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=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376the group of atoms that you are calculating the Gyration Tensor forLABEL=a label for the action so that its output can be referenced in the input to other actionsrg_1The GYRATION action with labelrg_1calculates the following quantities:

QuantityTypeDescriptionrg_1 scalar the radius of gyration 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=434,459,492,516,540,573,598,624,653,677,701,724,749,775,804the group of atoms that you are calculating the Gyration Tensor forLABEL=a label for the action so that its output can be referenced in the input to other actionsrg_2The GYRATION action with labelrg_2calculates the following quantities:

QuantityTypeDescriptionrg_2 scalar the radius of gyration

# hydrophobic residuesCOMCalculate the center of mass for a group of atoms. More detailsATOMS=31-63the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH1The COM action with labelH1calculates the following quantities:

QuantityTypeDescriptionH1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=112-144the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH2The COM action with labelH2calculates the following quantities:

QuantityTypeDescriptionH2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=196-224the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH3The COM action with labelH3calculates the following quantities:

QuantityTypeDescriptionH3 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=273-295the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH4The COM action with labelH4calculates the following quantities:

QuantityTypeDescriptionH4 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=347-375the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH5The COM action with labelH5calculates the following quantities:

QuantityTypeDescriptionH5 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=459-491the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH1_2The COM action with labelH1_2calculates the following quantities:

QuantityTypeDescriptionH1_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=540-572the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH2_2The COM action with labelH2_2calculates the following quantities:

QuantityTypeDescriptionH2_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=624-652the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH3_2The COM action with labelH3_2calculates the following quantities:

QuantityTypeDescriptionH3_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=701-723the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH4_2The COM action with labelH4_2calculates the following quantities:

QuantityTypeDescriptionH4_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=775-803the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionsH5_2The COM action with labelH5_2calculates the following quantities:

QuantityTypeDescriptionH5_2 atoms virtual atom calculated by COM action COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=First list of atomsH1,H2,H3,H4,H5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)H1_2,H2_2,H3_2,H4_2,H5_2R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=a label for the action so that its output can be referenced in the input to other actionsCOORDThe COORDINATION action with labelCOORDcalculates the following quantities:

QuantityTypeDescriptionCOORD scalar the value of the coordination COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More detailsGROUPA=First list of atomsH1,H2,H3,H4,H5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)H1_2,H2_2,H3_2,H4_2,H5_2R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=a label for the action so that its output can be referenced in the input to other actionsCOORDD_0=0.0The d_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=First list of atomsH1,H2,H3,H4,H5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)H5_2,H4_2,H3_2,H2_2,H1_2R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=a label for the action so that its output can be referenced in the input to other actionsPAIRThe COORDINATION action with labelPAIRcalculates the following quantities:

QuantityTypeDescriptionPAIR scalar the value of the coordination COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=First list of atomsH1,H2,H3,H4,H5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)H5_2,H4_2,H3_2,H2_2,H1_2R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=a label for the action so that its output can be referenced in the input to other actionsPAIRD_0=0.0The d_0 parameter of the switching functionINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=dihedral.dat # The command: # INCLUDE FILE=dihedral.dat # ensures PLUMED loads the contents of the file called dihedral.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included

# dihedrals # phi: CLP-,N,CA,C

The INCLUDE action with labeldihedral.datcalculates somethingphi1The TORSION action with labelphi1calculates the following quantities::

QuantityTypeDescriptionphi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=29,31,59,62the four atoms involved in the torsional anglephi2The TORSION action with labelphi2calculates the following quantities::

QuantityTypeDescriptionphi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=62,64,83,86the four atoms involved in the torsional anglephi3The TORSION action with labelphi3calculates the following quantities::

QuantityTypeDescriptionphi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=86,88,107,110the four atoms involved in the torsional anglephi4The TORSION action with labelphi4calculates the following quantities::

QuantityTypeDescriptionphi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=110,112,140,143the four atoms involved in the torsional anglephi5The TORSION action with labelphi5calculates the following quantities::

QuantityTypeDescriptionphi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=143,145,165,168the four atoms involved in the torsional anglephi6The TORSION action with labelphi6calculates the following quantities::

QuantityTypeDescriptionphi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=168,170,191,194the four atoms involved in the torsional anglephi7The TORSION action with labelphi7calculates the following quantities::

QuantityTypeDescriptionphi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=194,196,220,223the four atoms involved in the torsional anglephi8The TORSION action with labelphi8calculates the following quantities::

QuantityTypeDescriptionphi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=223,225,244,247the four atoms involved in the torsional anglephi9The TORSION action with labelphi9calculates the following quantities::

QuantityTypeDescriptionphi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=247,249,268,271the four atoms involved in the torsional anglephi10The TORSION action with labelphi10calculates the following quantities::

QuantityTypeDescriptionphi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=271,273,291,294the four atoms involved in the torsional anglephi11The TORSION action with labelphi11calculates the following quantities::

QuantityTypeDescriptionphi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=294,296,316,319the four atoms involved in the torsional anglephi12The TORSION action with labelphi12calculates the following quantities::

QuantityTypeDescriptionphi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=319,321,342,345the four atoms involved in the torsional anglephi13The TORSION action with labelphi13calculates the following quantities::

QuantityTypeDescriptionphi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=345,347,371,374the four atoms involved in the torsional anglephi14The TORSION action with labelphi14calculates the following quantities::

QuantityTypeDescriptionphi14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=374,376,395,398the four atoms involved in the torsional anglephi17The TORSION action with labelphi17calculates the following quantities::

QuantityTypeDescriptionphi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=457,459,487,490the four atoms involved in the torsional anglephi18The TORSION action with labelphi18calculates the following quantities::

QuantityTypeDescriptionphi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=490,492,511,514the four atoms involved in the torsional anglephi19The TORSION action with labelphi19calculates the following quantities::

QuantityTypeDescriptionphi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=514,516,535,538the four atoms involved in the torsional anglephi20The TORSION action with labelphi20calculates the following quantities::

QuantityTypeDescriptionphi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=538,540,568,571the four atoms involved in the torsional anglephi21The TORSION action with labelphi21calculates the following quantities::

QuantityTypeDescriptionphi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=571,573,593,596the four atoms involved in the torsional anglephi22The TORSION action with labelphi22calculates the following quantities::

QuantityTypeDescriptionphi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=596,598,619,622the four atoms involved in the torsional anglephi23The TORSION action with labelphi23calculates the following quantities::

QuantityTypeDescriptionphi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=622,624,648,651the four atoms involved in the torsional anglephi24The TORSION action with labelphi24calculates the following quantities::

QuantityTypeDescriptionphi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=651,653,672,675the four atoms involved in the torsional anglephi25The TORSION action with labelphi25calculates the following quantities::

QuantityTypeDescriptionphi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=675,677,696,699the four atoms involved in the torsional anglephi26The TORSION action with labelphi26calculates the following quantities::

QuantityTypeDescriptionphi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=699,701,719,722the four atoms involved in the torsional anglephi27The TORSION action with labelphi27calculates the following quantities::

QuantityTypeDescriptionphi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=722,724,744,747the four atoms involved in the torsional anglephi28The TORSION action with labelphi28calculates the following quantities::

QuantityTypeDescriptionphi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=747,749,770,773the four atoms involved in the torsional anglephi29The TORSION action with labelphi29calculates the following quantities::

QuantityTypeDescriptionphi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=773,775,799,802the four atoms involved in the torsional anglephi30The TORSION action with labelphi30calculates the following quantities::

QuantityTypeDescriptionphi30 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=802,804,819,822the four atoms involved in the torsional angle

# psi: NL,CA,CLP,NL+psi0The TORSION action with labelpsi0calculates the following quantities::

QuantityTypeDescriptionpsi0 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=1,26,29,31the four atoms involved in the torsional anglepsi1The TORSION action with labelpsi1calculates the following quantities::

QuantityTypeDescriptionpsi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,59,62,64the four atoms involved in the torsional anglepsi2The TORSION action with labelpsi2calculates the following quantities::

QuantityTypeDescriptionpsi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=64,83,86,88the four atoms involved in the torsional anglepsi3The TORSION action with labelpsi3calculates the following quantities::

QuantityTypeDescriptionpsi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=88,107,110,112the four atoms involved in the torsional anglepsi4The TORSION action with labelpsi4calculates the following quantities::

QuantityTypeDescriptionpsi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,140,143,145the four atoms involved in the torsional anglepsi5The TORSION action with labelpsi5calculates the following quantities::

QuantityTypeDescriptionpsi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=145,165,168,170the four atoms involved in the torsional anglepsi6The TORSION action with labelpsi6calculates the following quantities::

QuantityTypeDescriptionpsi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=170,191,194,196the four atoms involved in the torsional anglepsi7The TORSION action with labelpsi7calculates the following quantities::

QuantityTypeDescriptionpsi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,220,223,225the four atoms involved in the torsional anglepsi8The TORSION action with labelpsi8calculates the following quantities::

QuantityTypeDescriptionpsi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=225,244,247,249the four atoms involved in the torsional anglepsi9The TORSION action with labelpsi9calculates the following quantities::

QuantityTypeDescriptionpsi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=249,268,271,273the four atoms involved in the torsional anglepsi10The TORSION action with labelpsi10calculates the following quantities::

QuantityTypeDescriptionpsi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,291,294,296the four atoms involved in the torsional anglepsi11The TORSION action with labelpsi11calculates the following quantities::

QuantityTypeDescriptionpsi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=296,316,319,321the four atoms involved in the torsional anglepsi12The TORSION action with labelpsi12calculates the following quantities::

QuantityTypeDescriptionpsi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=321,342,345,347the four atoms involved in the torsional anglepsi13The TORSION action with labelpsi13calculates the following quantities::

QuantityTypeDescriptionpsi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,371,374,376the four atoms involved in the torsional anglepsi16The TORSION action with labelpsi16calculates the following quantities::

QuantityTypeDescriptionpsi16 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=434,454,457,459the four atoms involved in the torsional anglepsi17The TORSION action with labelpsi17calculates the following quantities::

QuantityTypeDescriptionpsi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,487,490,492the four atoms involved in the torsional anglepsi18The TORSION action with labelpsi18calculates the following quantities::

QuantityTypeDescriptionpsi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=492,511,514,516the four atoms involved in the torsional anglepsi19The TORSION action with labelpsi19calculates the following quantities::

QuantityTypeDescriptionpsi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=516,535,538,540the four atoms involved in the torsional anglepsi20The TORSION action with labelpsi20calculates the following quantities::

QuantityTypeDescriptionpsi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,568,571,573the four atoms involved in the torsional anglepsi21The TORSION action with labelpsi21calculates the following quantities::

QuantityTypeDescriptionpsi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=573,593,596,598the four atoms involved in the torsional anglepsi22The TORSION action with labelpsi22calculates the following quantities::

QuantityTypeDescriptionpsi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=598,619,622,624the four atoms involved in the torsional anglepsi23The TORSION action with labelpsi23calculates the following quantities::

QuantityTypeDescriptionpsi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,648,651,653the four atoms involved in the torsional anglepsi24The TORSION action with labelpsi24calculates the following quantities::

QuantityTypeDescriptionpsi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=653,672,675,677the four atoms involved in the torsional anglepsi25The TORSION action with labelpsi25calculates the following quantities::

QuantityTypeDescriptionpsi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=677,696,699,701the four atoms involved in the torsional anglepsi26The TORSION action with labelpsi26calculates the following quantities::

QuantityTypeDescriptionpsi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,719,722,724the four atoms involved in the torsional anglepsi27The TORSION action with labelpsi27calculates the following quantities::

QuantityTypeDescriptionpsi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=724,744,747,749the four atoms involved in the torsional anglepsi28The TORSION action with labelpsi28calculates the following quantities::

QuantityTypeDescriptionpsi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=749,770,773,775the four atoms involved in the torsional anglepsi29The TORSION action with labelpsi29calculates the following quantities::

QuantityTypeDescriptionpsi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=775,799,802,804the four atoms involved in the torsional angle

# omega: CA-, C-, N, CAomega1The TORSION action with labelomega1calculates the following quantities::

QuantityTypeDescriptionomega1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=26,29,31,59the four atoms involved in the torsional angleomega2The TORSION action with labelomega2calculates the following quantities::

QuantityTypeDescriptionomega2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,62,64,83the four atoms involved in the torsional angleomega3The TORSION action with labelomega3calculates the following quantities::

QuantityTypeDescriptionomega3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,86,88,107the four atoms involved in the torsional angleomega4The TORSION action with labelomega4calculates the following quantities::

QuantityTypeDescriptionomega4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,110,112,140the four atoms involved in the torsional angleomega5The TORSION action with labelomega5calculates the following quantities::

QuantityTypeDescriptionomega5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,143,145,165the four atoms involved in the torsional angleomega6The TORSION action with labelomega6calculates the following quantities::

QuantityTypeDescriptionomega6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,168,170,191the four atoms involved in the torsional angleomega7The TORSION action with labelomega7calculates the following quantities::

QuantityTypeDescriptionomega7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,194,196,220the four atoms involved in the torsional angleomega8The TORSION action with labelomega8calculates the following quantities::

QuantityTypeDescriptionomega8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,223,225,244the four atoms involved in the torsional angleomega9The TORSION action with labelomega9calculates the following quantities::

QuantityTypeDescriptionomega9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,247,249,268the four atoms involved in the torsional angleomega10The TORSION action with labelomega10calculates the following quantities::

QuantityTypeDescriptionomega10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,271,273,291the four atoms involved in the torsional angleomega11The TORSION action with labelomega11calculates the following quantities::

QuantityTypeDescriptionomega11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,294,296,316the four atoms involved in the torsional angleomega12The TORSION action with labelomega12calculates the following quantities::

QuantityTypeDescriptionomega12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,319,321,342the four atoms involved in the torsional angleomega13The TORSION action with labelomega13calculates the following quantities::

QuantityTypeDescriptionomega13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,345,347,371the four atoms involved in the torsional angleomega14The TORSION action with labelomega14calculates the following quantities::

QuantityTypeDescriptionomega14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,374,376,395the four atoms involved in the torsional angleomega17The TORSION action with labelomega17calculates the following quantities::

QuantityTypeDescriptionomega17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,457,459,487the four atoms involved in the torsional angleomega18The TORSION action with labelomega18calculates the following quantities::

QuantityTypeDescriptionomega18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,490,492,511the four atoms involved in the torsional angleomega19The TORSION action with labelomega19calculates the following quantities::

QuantityTypeDescriptionomega19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,514,516,535the four atoms involved in the torsional angleomega20The TORSION action with labelomega20calculates the following quantities::

QuantityTypeDescriptionomega20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,538,540,568the four atoms involved in the torsional angleomega21The TORSION action with labelomega21calculates the following quantities::

QuantityTypeDescriptionomega21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,571,573,593the four atoms involved in the torsional angleomega22The TORSION action with labelomega22calculates the following quantities::

QuantityTypeDescriptionomega22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,596,598,619the four atoms involved in the torsional angleomega23The TORSION action with labelomega23calculates the following quantities::

QuantityTypeDescriptionomega23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,622,624,648the four atoms involved in the torsional angleomega24The TORSION action with labelomega24calculates the following quantities::

QuantityTypeDescriptionomega24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,651,653,672the four atoms involved in the torsional angleomega25The TORSION action with labelomega25calculates the following quantities::

QuantityTypeDescriptionomega25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,675,677,696the four atoms involved in the torsional angleomega26The TORSION action with labelomega26calculates the following quantities::

QuantityTypeDescriptionomega26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,699,701,719the four atoms involved in the torsional angleomega27The TORSION action with labelomega27calculates the following quantities::

QuantityTypeDescriptionomega27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,722,724,744the four atoms involved in the torsional angleomega28The TORSION action with labelomega28calculates the following quantities::

QuantityTypeDescriptionomega28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,747,749,770the four atoms involved in the torsional angleomega29The TORSION action with labelomega29calculates the following quantities::

QuantityTypeDescriptionomega29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,773,775,799the four atoms involved in the torsional angleomega30The TORSION action with labelomega30calculates the following quantities::

QuantityTypeDescriptionomega30 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=799,802,804,819the four atoms involved in the torsional angle

# chi 1 dihedral: CA, NL, CB1, CG (or other)chi1The TORSION action with labelchi1calculates the following quantities::

QuantityTypeDescriptionchi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,31,32,35the four atoms involved in the torsional anglechi2The TORSION action with labelchi2calculates the following quantities::

QuantityTypeDescriptionchi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,64,65,71the four atoms involved in the torsional anglechi3The TORSION action with labelchi3calculates the following quantities::

QuantityTypeDescriptionchi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,88,89,95the four atoms involved in the torsional anglechi4The TORSION action with labelchi4calculates the following quantities::

QuantityTypeDescriptionchi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,112,113,116the four atoms involved in the torsional anglechi5The TORSION action with labelchi5calculates the following quantities::

QuantityTypeDescriptionchi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,145,146,152the four atoms involved in the torsional anglechi6The TORSION action with labelchi6calculates the following quantities::

QuantityTypeDescriptionchi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,170,171,177the four atoms involved in the torsional anglechi7The TORSION action with labelchi7calculates the following quantities::

QuantityTypeDescriptionchi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,196,197,203the four atoms involved in the torsional anglechi8The TORSION action with labelchi8calculates the following quantities::

QuantityTypeDescriptionchi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,225,226,232the four atoms involved in the torsional anglechi9The TORSION action with labelchi9calculates the following quantities::

QuantityTypeDescriptionchi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,249,250,256the four atoms involved in the torsional anglechi10The TORSION action with labelchi10calculates the following quantities::

QuantityTypeDescriptionchi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,273,274,280the four atoms involved in the torsional anglechi11The TORSION action with labelchi11calculates the following quantities::

QuantityTypeDescriptionchi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,296,297,303the four atoms involved in the torsional anglechi12The TORSION action with labelchi12calculates the following quantities::

QuantityTypeDescriptionchi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,321,322,328the four atoms involved in the torsional anglechi13The TORSION action with labelchi13calculates the following quantities::

QuantityTypeDescriptionchi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,347,348,354the four atoms involved in the torsional anglechi14The TORSION action with labelchi14calculates the following quantities::

QuantityTypeDescriptionchi14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=395,376,377,383the four atoms involved in the torsional anglechi16The TORSION action with labelchi16calculates the following quantities::

QuantityTypeDescriptionchi16 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,434,435,441the four atoms involved in the torsional anglechi17The TORSION action with labelchi17calculates the following quantities::

QuantityTypeDescriptionchi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,459,460,463the four atoms involved in the torsional anglechi18The TORSION action with labelchi18calculates the following quantities::

QuantityTypeDescriptionchi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,492,493,499the four atoms involved in the torsional anglechi19The TORSION action with labelchi19calculates the following quantities::

QuantityTypeDescriptionchi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,516,517,523the four atoms involved in the torsional anglechi20The TORSION action with labelchi20calculates the following quantities::

QuantityTypeDescriptionchi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,540,541,544the four atoms involved in the torsional anglechi21The TORSION action with labelchi21calculates the following quantities::

QuantityTypeDescriptionchi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,573,574,580the four atoms involved in the torsional anglechi22The TORSION action with labelchi22calculates the following quantities::

QuantityTypeDescriptionchi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,598,599,605the four atoms involved in the torsional anglechi23The TORSION action with labelchi23calculates the following quantities::

QuantityTypeDescriptionchi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,624,625,631the four atoms involved in the torsional anglechi24The TORSION action with labelchi24calculates the following quantities::

QuantityTypeDescriptionchi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,653,654,660the four atoms involved in the torsional anglechi25The TORSION action with labelchi25calculates the following quantities::

QuantityTypeDescriptionchi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,677,678,684the four atoms involved in the torsional anglechi26The TORSION action with labelchi26calculates the following quantities::

QuantityTypeDescriptionchi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,701,702,708the four atoms involved in the torsional anglechi27The TORSION action with labelchi27calculates the following quantities::

QuantityTypeDescriptionchi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,724,725,731the four atoms involved in the torsional anglechi28The TORSION action with labelchi28calculates the following quantities::

QuantityTypeDescriptionchi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,749,750,756the four atoms involved in the torsional anglechi29The TORSION action with labelchi29calculates the following quantities::

QuantityTypeDescriptionchi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=799,775,776,782the four atoms involved in the torsional angle

# chi 2 dihedral: NL,CB1,CG,CD1chiaThe TORSION action with labelchiacalculates the following quantities::

QuantityTypeDescriptionchia scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,32,35,37the four atoms involved in the torsional anglechibThe TORSION action with labelchibcalculates the following quantities::

QuantityTypeDescriptionchib scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,113,116,118the four atoms involved in the torsional anglechicThe TORSION action with labelchiccalculates the following quantities::

QuantityTypeDescriptionchic scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,197,203,205the four atoms involved in the torsional anglechidThe TORSION action with labelchidcalculates the following quantities::

QuantityTypeDescriptionchid scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,274,280,281the four atoms involved in the torsional anglechieThe TORSION action with labelchiecalculates the following quantities::

QuantityTypeDescriptionchie scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,348,354,356the four atoms involved in the torsional anglechifThe TORSION action with labelchifcalculates the following quantities::

QuantityTypeDescriptionchif scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,460,463,465the four atoms involved in the torsional anglechigThe TORSION action with labelchigcalculates the following quantities::

QuantityTypeDescriptionchig scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,541,544,546the four atoms involved in the torsional anglechihThe TORSION action with labelchihcalculates the following quantities::

QuantityTypeDescriptionchih scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,625,631,633the four atoms involved in the torsional anglechiiThe TORSION action with labelchiicalculates the following quantities::

QuantityTypeDescriptionchii scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,702,708,709the four atoms involved in the torsional anglechijThe TORSION action with labelchijcalculates the following quantities::

QuantityTypeDescriptionchij scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=775,776,782,784the four atoms involved in the torsional angle

# chi 3 dihedral: CB1, CG, CC, CD1 just for NDPEschiaaThe TORSION action with labelchiaacalculates the following quantities::

QuantityTypeDescriptionchiaa scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=32,35,37,38the four atoms involved in the torsional anglechibaThe TORSION action with labelchibacalculates the following quantities::

QuantityTypeDescriptionchiba scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=113,116,118,119the four atoms involved in the torsional anglechifaThe TORSION action with labelchifacalculates the following quantities::

QuantityTypeDescriptionchifa scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=460,463,465,466the four atoms involved in the torsional anglechigaThe TORSION action with labelchigacalculates the following quantities::

QuantityTypeDescriptionchiga scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=541,544,546,547 # --- End of included input ---the four atoms involved in the torsional angleINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=alphabeta.dat # The command: # INCLUDE FILE=alphabeta.dat # ensures PLUMED loads the contents of the file called alphabeta.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included

# updated dihedrals 1/12/23 # phi: CLP-,NL,CA,CLP # positive 1.57 is alpha d plus, negative is alpha d minus The INCLUDE action with labelalphabeta.datcalculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=29,31,59,62the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.40the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.40the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.40the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.40the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.40the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.40the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.40the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.40the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.40the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.40the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.40the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.40the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.40the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.40the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_PHI0The SUM action with labelAB_PHI0calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_PHI0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.40the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.40the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.40the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.40the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.40the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.40the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.40the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.40the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.40the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.40the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.40the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.40the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.40the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.40the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_PHI1The SUM action with labelAB_PHI1calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_PHI1 scalar the sum of all the elements in the input vector

# psi: NL,CA,CLP,NL+ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.97the reference values for each of the torsional anglesATOMS2=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.97the reference values for each of the torsional anglesATOMS3=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.97the reference values for each of the torsional anglesATOMS4=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.97the reference values for each of the torsional anglesATOMS5=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.97the reference values for each of the torsional anglesATOMS6=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.97the reference values for each of the torsional anglesATOMS7=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.97the reference values for each of the torsional anglesATOMS8=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.97the reference values for each of the torsional anglesATOMS9=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.97the reference values for each of the torsional anglesATOMS10=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.97the reference values for each of the torsional anglesATOMS11=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.97the reference values for each of the torsional anglesATOMS12=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE12=2.97the reference values for each of the torsional anglesATOMS13=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE13=2.97the reference values for each of the torsional anglesATOMS14=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE14=2.97the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_PSI0The SUM action with labelAB_PSI0calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_PSI0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.97the reference values for each of the torsional anglesATOMS2=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.97the reference values for each of the torsional anglesATOMS3=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.97the reference values for each of the torsional anglesATOMS4=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.97the reference values for each of the torsional anglesATOMS5=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.97the reference values for each of the torsional anglesATOMS6=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.97the reference values for each of the torsional anglesATOMS7=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.97the reference values for each of the torsional anglesATOMS8=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.97the reference values for each of the torsional anglesATOMS9=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.97the reference values for each of the torsional anglesATOMS10=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.97the reference values for each of the torsional anglesATOMS11=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.97the reference values for each of the torsional anglesATOMS12=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE12=2.97the reference values for each of the torsional anglesATOMS13=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE13=2.97the reference values for each of the torsional anglesATOMS14=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE14=2.97the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_PSI1The SUM action with labelAB_PSI1calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_PSI1 scalar the sum of all the elements in the input vector

# omega: CA-, C-, N, CAALPHABETA...Calculate the alpha beta CV More detailsATOMS1=26,29,31,59the atoms involved for each of the torsions you wish to calculateREFERENCE1=0the reference values for each of the torsional anglesATOMS2=59,62,64,83the atoms involved for each of the torsions you wish to calculateREFERENCE2=0the reference values for each of the torsional anglesATOMS3=83,86,88,107the atoms involved for each of the torsions you wish to calculateREFERENCE3=0the reference values for each of the torsional anglesATOMS4=107,110,112,140the atoms involved for each of the torsions you wish to calculateREFERENCE4=0the reference values for each of the torsional anglesATOMS5=140,143,145,165the atoms involved for each of the torsions you wish to calculateREFERENCE5=0the reference values for each of the torsional anglesATOMS6=165,168,170,191the atoms involved for each of the torsions you wish to calculateREFERENCE6=0the reference values for each of the torsional anglesATOMS7=191,194,196,220the atoms involved for each of the torsions you wish to calculateREFERENCE7=0the reference values for each of the torsional anglesATOMS8=220,223,225,244the atoms involved for each of the torsions you wish to calculateREFERENCE8=0the reference values for each of the torsional anglesATOMS9=244,247,249,268the atoms involved for each of the torsions you wish to calculateREFERENCE9=0the reference values for each of the torsional anglesATOMS10=268,271,273,291the atoms involved for each of the torsions you wish to calculateREFERENCE10=0the reference values for each of the torsional anglesATOMS11=291,294,296,316the atoms involved for each of the torsions you wish to calculateREFERENCE11=0the reference values for each of the torsional anglesATOMS12=316,319,321,342the atoms involved for each of the torsions you wish to calculateREFERENCE12=0the reference values for each of the torsional anglesATOMS13=342,345,347,371the atoms involved for each of the torsions you wish to calculateREFERENCE13=0the reference values for each of the torsional anglesATOMS14=371,374,376,395the atoms involved for each of the torsions you wish to calculateREFERENCE14=0the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_O0The SUM action with labelAB_O0calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_O0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=454,457,459,487the atoms involved for each of the torsions you wish to calculateREFERENCE1=0the reference values for each of the torsional anglesATOMS2=487,490,492,511the atoms involved for each of the torsions you wish to calculateREFERENCE2=0the reference values for each of the torsional anglesATOMS3=511,514,516,535the atoms involved for each of the torsions you wish to calculateREFERENCE3=0the reference values for each of the torsional anglesATOMS4=535,538,540,568the atoms involved for each of the torsions you wish to calculateREFERENCE4=0the reference values for each of the torsional anglesATOMS5=568,571,573,593the atoms involved for each of the torsions you wish to calculateREFERENCE5=0the reference values for each of the torsional anglesATOMS6=593,596,598,619the atoms involved for each of the torsions you wish to calculateREFERENCE6=0the reference values for each of the torsional anglesATOMS7=619,622,624,648the atoms involved for each of the torsions you wish to calculateREFERENCE7=0the reference values for each of the torsional anglesATOMS8=648,651,653,672the atoms involved for each of the torsions you wish to calculateREFERENCE8=0the reference values for each of the torsional anglesATOMS9=672,675,677,696the atoms involved for each of the torsions you wish to calculateREFERENCE9=0the reference values for each of the torsional anglesATOMS10=696,699,701,719the atoms involved for each of the torsions you wish to calculateREFERENCE10=0the reference values for each of the torsional anglesATOMS11=719,722,724,744the atoms involved for each of the torsions you wish to calculateREFERENCE11=0the reference values for each of the torsional anglesATOMS12=744,747,749,770the atoms involved for each of the torsions you wish to calculateREFERENCE12=0the reference values for each of the torsional anglesATOMS13=770,773,775,799the atoms involved for each of the torsions you wish to calculateREFERENCE13=0the reference values for each of the torsional anglesATOMS14=799,802,804,819the atoms involved for each of the torsions you wish to calculateREFERENCE14=0the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_O1The SUM action with labelAB_O1calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_O1 scalar the sum of all the elements in the input vector

# --- End of included input ---INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=minima.dat # The command: # INCLUDE FILE=minima.dat # ensures PLUMED loads the contents of the file called minima.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included

# phi = positive 1.57 is alpha d plus, negative is alpha d minus # psi = 3.14, omega = 0

# first helix The INCLUDE action with labelminima.datcalculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=29,31,59,62the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.40the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.40the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.40the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.40the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.40the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.40the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.40the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.40the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.40the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.40the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.40the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.40the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.40the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.40the reference values for each of the torsional anglesATOMS15=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE15=2.97the reference values for each of the torsional anglesATOMS16=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE16=2.97the reference values for each of the torsional anglesATOMS17=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE17=2.97the reference values for each of the torsional anglesATOMS18=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE18=2.97the reference values for each of the torsional anglesATOMS19=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE19=2.97the reference values for each of the torsional anglesATOMS20=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE20=2.97the reference values for each of the torsional anglesATOMS21=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE21=2.97the reference values for each of the torsional anglesATOMS22=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE22=2.97the reference values for each of the torsional anglesATOMS23=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE23=2.97the reference values for each of the torsional anglesATOMS24=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE24=2.97the reference values for each of the torsional anglesATOMS25=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE25=2.97the reference values for each of the torsional anglesATOMS26=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE26=2.97the reference values for each of the torsional anglesATOMS27=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE27=2.97the reference values for each of the torsional anglesATOMS28=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE28=2.97the reference values for each of the torsional anglesATOMS29=26,29,31,59the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=59,62,64,83the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=83,86,88,107the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=107,110,112,140the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=140,143,145,165the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=165,168,170,191the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesATOMS35=191,194,196,220the atoms involved for each of the torsions you wish to calculateREFERENCE35=0the reference values for each of the torsional anglesATOMS36=220,223,225,244the atoms involved for each of the torsions you wish to calculateREFERENCE36=0the reference values for each of the torsional anglesATOMS37=244,247,249,268the atoms involved for each of the torsions you wish to calculateREFERENCE37=0the reference values for each of the torsional anglesATOMS38=268,271,273,291the atoms involved for each of the torsions you wish to calculateREFERENCE38=0the reference values for each of the torsional anglesATOMS39=291,294,296,316the atoms involved for each of the torsions you wish to calculateREFERENCE39=0the reference values for each of the torsional anglesATOMS40=316,319,321,342the atoms involved for each of the torsions you wish to calculateREFERENCE40=0the reference values for each of the torsional anglesATOMS41=342,345,347,371the atoms involved for each of the torsions you wish to calculateREFERENCE41=0the reference values for each of the torsional anglesATOMS42=371,374,376,395the atoms involved for each of the torsions you wish to calculateREFERENCE42=0the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_1The SUM action with labelAB_1calculates the following quantities:... ALPHABETA

QuantityTypeDescriptionAB_1 scalar the sum of all the elements in the input vector

#second helixALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.40the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.40the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.40the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.40the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.40the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.40the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.40the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.40the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.40the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.40the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.40the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.40the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.40the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.40the reference values for each of the torsional anglesATOMS15=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE15=2.97the reference values for each of the torsional anglesATOMS16=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE16=2.97the reference values for each of the torsional anglesATOMS17=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE17=2.97the reference values for each of the torsional anglesATOMS18=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE18=2.97the reference values for each of the torsional anglesATOMS19=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE19=2.97the reference values for each of the torsional anglesATOMS20=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE20=2.97the reference values for each of the torsional anglesATOMS21=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE21=2.97the reference values for each of the torsional anglesATOMS22=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE22=2.97the reference values for each of the torsional anglesATOMS23=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE23=2.97the reference values for each of the torsional anglesATOMS24=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE24=2.97the reference values for each of the torsional anglesATOMS25=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE25=2.97the reference values for each of the torsional anglesATOMS26=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE26=2.97the reference values for each of the torsional anglesATOMS27=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE27=2.97the reference values for each of the torsional anglesATOMS28=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE28=2.97the reference values for each of the torsional anglesATOMS29=454,457,459,487the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=487,490,492,511the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=511,514,516,535the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=535,538,540,568the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=568,571,573,593the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=593,596,598,619the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesATOMS35=619,622,624,648the atoms involved for each of the torsions you wish to calculateREFERENCE35=0the reference values for each of the torsional anglesATOMS36=648,651,653,672the atoms involved for each of the torsions you wish to calculateREFERENCE36=0the reference values for each of the torsional anglesATOMS37=672,675,677,696the atoms involved for each of the torsions you wish to calculateREFERENCE37=0the reference values for each of the torsional anglesATOMS38=696,699,701,719the atoms involved for each of the torsions you wish to calculateREFERENCE38=0the reference values for each of the torsional anglesATOMS39=719,722,724,744the atoms involved for each of the torsions you wish to calculateREFERENCE39=0the reference values for each of the torsional anglesATOMS40=744,747,749,770the atoms involved for each of the torsions you wish to calculateREFERENCE40=0the reference values for each of the torsional anglesATOMS41=770,773,775,799the atoms involved for each of the torsions you wish to calculateREFERENCE41=0the reference values for each of the torsional anglesATOMS42=799,802,804,819the atoms involved for each of the torsions you wish to calculateREFERENCE42=0the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsAB_2The SUM action with labelAB_2calculates the following quantities:... ALPHABETA # --- End of included input ---

QuantityTypeDescriptionAB_2 scalar the sum of all the elements in the input vector MOVINGRESTRAINT...Add a time-dependent, harmonic restraint on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd,AB_1,AB_2,AB_PHI0,AB_PHI1,AB_PSI0,AB_PSI1,AB_O0,AB_O1STEP0=50000This keyword appears multiple times as STEPx with x=0,1,2,AT0=2,28,23,8,6,13,12,6,4ATx is equal to the position of the restraint at time STEPxKAPPA0=1000,100,100,100,100,100,100,100,100KAPPAx is equal to the value of the force constants at time STEPxSTEP1=2550000This keyword appears multiple times as STEPx with x=0,1,2,AT1=4,42,42,14,14,14,14,14,14ATx is equal to the position of the restraint at time STEPxKAPPA1=2500,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP2=8825000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA2=0,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP3=25100000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA3=0,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP4=37500000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA4=0,0,0,0,0,0,0,0,0 ... MOVINGRESTRAINTKAPPAx is equal to the value of the force constants at time STEPxPrint 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