Project ID: plumID:24.033
Source: Plumed-nest/7q4b/plumed_analysis.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
#RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=structure_renumbered.pdb

# Define all heavy atoms using GROMACS index file
system: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System
protein-h: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
Protein-noASPGLU-noH: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H_&_!GLU_ASP_&_OE1_OE2_OD1_OD2

# Constrain the protein CA protofibril core
RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=structure_renumbered.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL LABELa label for the action so that its output can be referenced in the input to other actions=rmsd
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=0.0 EXP the powers for the walls=3 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=rmsdwall

# Make protein whole: add reference position of first heavy atom (in nm)
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-627 ENTITY1the atoms that make up a molecule that you wish to align=628-1254 ENTITY2the atoms that make up a molecule that you wish to align=1255-1881 ENTITY3the atoms that make up a molecule that you wish to align=1882-2508 ENTITY4the atoms that make up a molecule that you wish to align=2509-3135 ENTITY5the atoms that make up a molecule that you wish to align=3136-3762 ENTITY6the atoms that make up a molecule that you wish to align=3763-4389 ENTITY7the atoms that make up a molecule that you wish to align=4390-5016 ENTITY8the atoms that make up a molecule that you wish to align=5017-5643 ENTITY9the atoms that make up a molecule that you wish to align=5644-6270 ENTITY10the atoms that make up a molecule that you wish to align=6271-6897 ENTITY11the atoms that make up a molecule that you wish to align=6898-7524 ENTITY12the atoms that make up a molecule that you wish to align=7525-8151 ENTITY13the atoms that make up a molecule that you wish to align=8152-8778 ENTITY14the atoms that make up a molecule that you wish to align=8779-9405 ENTITY15the atoms that make up a molecule that you wish to align=9406-10032 ENTITY16the atoms that make up a molecule that you wish to align=10033-10659 ENTITY17the atoms that make up a molecule that you wish to align=10660-11286 ENTITY18the atoms that make up a molecule that you wish to align=11287-11913 ENTITY19the atoms that make up a molecule that you wish to align=11914-12540 ENTITY20the atoms that make up a molecule that you wish to align=12541-13167 ENTITY21the atoms that make up a molecule that you wish to align=13168-13794 ENTITY22the atoms that make up a molecule that you wish to align=13795-14421 ENTITY23the atoms that make up a molecule that you wish to align=14422-15048 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file

# Definition of tails and epitopes
tail0: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail0
epitope0: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope0
tail4: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail4
epitope4: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope4
tail22: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail22
epitope22: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope22
tail2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail2
epitope2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope2
tail20: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail20
epitope20: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope20
tail6: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail6
epitope6: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope6
tail8: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail8
epitope8: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope8
tail14: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail14
epitope14: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope14
tail10: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail10
epitope10: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope10
tail12: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail12
epitope12: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope12
tail16: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail16
epitope16: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope16
tail18: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tail18
epitope18: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=epitope18

# Definition of the center of mass (CENTER) for tail and epitope
c_tail0: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail0
c_tail2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail2
c_tail4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail4
c_tail6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail6
c_tail8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail8
c_tail10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail10
c_tail12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail12
c_tail14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail14
c_tail16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail16
c_tail18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail18
c_tail20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail20
c_tail22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=tail22
c_epitope0: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope0
c_epitope2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope2
c_epitope4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope4
c_epitope6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope6
c_epitope8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope8
c_epitope10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope10
c_epitope12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope12
c_epitope14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope14
c_epitope16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope16
c_epitope18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope18
c_epitope20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope20
c_epitope22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=epitope22

# CV.1: Inter-tail contacts
con0: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail0 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail2 R_0The r_0 parameter of the switching function=0.8
con1: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail0 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail4 R_0The r_0 parameter of the switching function=0.8
con2: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail22 R_0The r_0 parameter of the switching function=0.8
con3: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail20 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail22 R_0The r_0 parameter of the switching function=0.8
con4: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail6 R_0The r_0 parameter of the switching function=0.8
con5: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail8 R_0The r_0 parameter of the switching function=0.8
con6: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail14 R_0The r_0 parameter of the switching function=0.8
con7: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail14 R_0The r_0 parameter of the switching function=0.8
con8: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail12 R_0The r_0 parameter of the switching function=0.8
con9: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail12 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail16 R_0The r_0 parameter of the switching function=0.8
con10: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=tail16 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail18 R_0The r_0 parameter of the switching function=0.8

# CV.2: Distance between CENTER of tials and epitopes
dcm_0: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail0,c_epitope0
dcm_2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail2,c_epitope2
dcm_4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail4,c_epitope4
dcm_6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail6,c_epitope6
dcm_8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail8,c_epitope8
dcm_10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail10,c_epitope10
dcm_12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail12,c_epitope12
dcm_14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail14,c_epitope14
dcm_16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail16,c_epitope16
dcm_18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail18,c_epitope18
dcm_20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail20,c_epitope20
dcm_22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_tail22,c_epitope22

# CV.3: alpha helical content in Tails
alpha0: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-8 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha2: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=85-92 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha4: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=169-176 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha6: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=253-260 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha8: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=337-344 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha10: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=421-428 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha14: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=589-596 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha12: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=505-512 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha16: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=673-680 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha18: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=757-764 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha20: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=841-848 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1
alpha22: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=925-932 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1

# CV.4: parallel beta sheet content in Tails
parabeta0: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-9 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta2: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=85-93 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta4: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=169-177 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta6: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=253-261 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta8: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=337-345 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta10: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=421-429 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta12: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=505-513 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta14: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=589-597 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta16: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=673-681 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta18: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=757-765 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta20: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=841-849 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
parabeta22: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=925-933 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1


PBMETADUsed to performed Parallel Bias metadynamics. More details ...
# Carlo's Biasfactor rule-of-thumb: 10 * sqrt(number of CVs)
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=56 HEIGHTthe height of the Gaussian hills, one for all biases=0.3 PACEthe frequency for hill addition, one for all biases=500000000 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR LABELa label for the action so that its output can be referenced in the input to other actions=pb GRID_WSTRIDEfrequency for dumping the grid=10000 SIGMAthe widths of the Gaussian hills=1000 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
ARGthe labels of the scalars on which the bias will act=con0,con1,con2,con3,con4,con5,con6,con7,con8,con9,con10,alpha0,parabeta0,dcm_0,alpha4,parabeta4,dcm_4,alpha22,parabeta22,dcm_22,alpha2,parabeta2,dcm_2,alpha20,parabeta20,dcm_20,alpha6,parabeta6,dcm_6,alpha8,parabeta8,dcm_8,alpha14,parabeta14,dcm_14,alpha10,parabeta10,dcm_10,alpha12,parabeta12,dcm_12,alpha16,parabeta16,dcm_16,alpha18,parabeta18,dcm_18
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05,0.01,0.01,0.05
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=1,1,1,1,1,1,1,1,1,1,1,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2
GRID_MINthe lower bounds for the grid=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
GRID_MAXthe upper bounds for the grid=100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0,10.0,10.0,30.0
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_con0,HILLS_con1,HILLS_con2,HILLS_con3,HILLS_con4,HILLS_con5,HILLS_con6,HILLS_con7,HILLS_con8,HILLS_con9,HILLS_con10,HILLS_alpha0,HILLS_parabeta0,HILLS_dcm_0,HILLS_alpha4,HILLS_parabeta4,HILLS_dcm_4,HILLS_alpha22,HILLS_parabeta22,HILLS_dcm_22,HILLS_alpha2,HILLS_parabeta2,HILLS_dcm_2,HILLS_alpha20,HILLS_parabeta20,HILLS_dcm_20,HILLS_alpha6,HILLS_parabeta6,HILLS_dcm_6,HILLS_alpha8,HILLS_parabeta8,HILLS_dcm_8,HILLS_alpha14,HILLS_parabeta14,HILLS_dcm_14,HILLS_alpha10,HILLS_parabeta10,HILLS_dcm_10,HILLS_alpha12,HILLS_parabeta12,HILLS_dcm_12,HILLS_alpha16,HILLS_parabeta16,HILLS_dcm_16,HILLS_alpha18,HILLS_parabeta18,HILLS_dcm_18
#GRID_RFILES=GRID_con0,GRID_con1,GRID_con2,GRID_con3,GRID_con4,GRID_con5,GRID_con6,GRID_con7,GRID_con8,GRID_con9,GRID_con10,GRID_alpha0,GRID_parabeta0,GRID_dcm_0,GRID_alpha4,GRID_parabeta4,GRID_dcm_4,GRID_alpha22,GRID_parabeta22,GRID_dcm_22,GRID_alpha2,GRID_parabeta2,GRID_dcm_2,GRID_alpha20,GRID_parabeta20,GRID_dcm_20,GRID_alpha6,GRID_parabeta6,GRID_dcm_6,GRID_alpha8,GRID_parabeta8,GRID_dcm_8,GRID_alpha14,GRID_parabeta14,GRID_dcm_14,GRID_alpha10,GRID_parabeta10,GRID_dcm_10,GRID_alpha12,GRID_parabeta12,GRID_dcm_12,GRID_alpha16,GRID_parabeta16,GRID_dcm_16,GRID_alpha18,GRID_parabeta18,GRID_dcm_18
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID_con0,GRID_con1,GRID_con2,GRID_con3,GRID_con4,GRID_con5,GRID_con6,GRID_con7,GRID_con8,GRID_con9,GRID_con10,GRID_alpha0,GRID_parabeta0,GRID_dcm_0,GRID_alpha4,GRID_parabeta4,GRID_dcm_4,GRID_alpha22,GRID_parabeta22,GRID_dcm_22,GRID_alpha2,GRID_parabeta2,GRID_dcm_2,GRID_alpha20,GRID_parabeta20,GRID_dcm_20,GRID_alpha6,GRID_parabeta6,GRID_dcm_6,GRID_alpha8,GRID_parabeta8,GRID_dcm_8,GRID_alpha14,GRID_parabeta14,GRID_dcm_14,GRID_alpha10,GRID_parabeta10,GRID_dcm_10,GRID_alpha12,GRID_parabeta12,GRID_dcm_12,GRID_alpha16,GRID_parabeta16,GRID_dcm_16,GRID_alpha18,GRID_parabeta18,GRID_dcm_18
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310
...

# print useful info to file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pb.bias FILEthe name of the file on which to output these quantities=FULLBIAS STRIDE the frequency with which the quantities of interest should be output=1