PLUMED-NEST

Project ID: plumID:24.033
Source: Plumed-nest/7q4b/plumed.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

#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
The MOLINFO action with label  calculates somethingsystem: 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
The GROUP action with label system calculates somethingprotein-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
The GROUP action with label protein-h calculates somethingProtein-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
The GROUP action with label Protein-noASPGLU-noH calculates somethingRMSDCalculate the RMSD with respect to a reference structure. 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
The RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputUPPER_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)
The UPPER_WALLS action with label rmsdwall calculates the following quantities:
 Quantity   
 Description  
rmsdwall.bias
the instantaneous value of the bias potential
rmsdwall.force2
the instantaneous value of the squared force due to this bias potentialWHOLEMOLECULESThis 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
The GROUP action with label tail0 calculates somethingepitope0: 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
The GROUP action with label epitope0 calculates somethingtail4: 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
The GROUP action with label tail4 calculates somethingepitope4: 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
The GROUP action with label epitope4 calculates somethingtail22: 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
The GROUP action with label tail22 calculates somethingepitope22: 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
The GROUP action with label epitope22 calculates somethingtail2: 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
The GROUP action with label tail2 calculates somethingepitope2: 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
The GROUP action with label epitope2 calculates somethingtail20: 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
The GROUP action with label tail20 calculates somethingepitope20: 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
The GROUP action with label epitope20 calculates somethingtail6: 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
The GROUP action with label tail6 calculates somethingepitope6: 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
The GROUP action with label epitope6 calculates somethingtail8: 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
The GROUP action with label tail8 calculates somethingepitope8: 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
The GROUP action with label epitope8 calculates somethingtail14: 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
The GROUP action with label tail14 calculates somethingepitope14: 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
The GROUP action with label epitope14 calculates somethingtail10: 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
The GROUP action with label tail10 calculates somethingepitope10: 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
The GROUP action with label epitope10 calculates somethingtail12: 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
The GROUP action with label tail12 calculates somethingepitope12: 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
The GROUP action with label epitope12 calculates somethingtail16: 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
The GROUP action with label tail16 calculates somethingepitope16: 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
The GROUP action with label epitope16 calculates somethingtail18: 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
The GROUP action with label tail18 calculates somethingepitope18: 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 (COM) for tail and epitope
The GROUP action with label epitope18 calculates somethingc_tail0: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail0
The COM action with label c_tail0 calculates somethingc_tail2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail2
The COM action with label c_tail2 calculates somethingc_tail4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail4
The COM action with label c_tail4 calculates somethingc_tail6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail6
The COM action with label c_tail6 calculates somethingc_tail8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail8
The COM action with label c_tail8 calculates somethingc_tail10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail10
The COM action with label c_tail10 calculates somethingc_tail12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail12
The COM action with label c_tail12 calculates somethingc_tail14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail14
The COM action with label c_tail14 calculates somethingc_tail16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail16
The COM action with label c_tail16 calculates somethingc_tail18: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail18
The COM action with label c_tail18 calculates somethingc_tail20: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail20
The COM action with label c_tail20 calculates somethingc_tail22: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tail22
The COM action with label c_tail22 calculates somethingc_epitope0: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope0
The COM action with label c_epitope0 calculates somethingc_epitope2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope2
The COM action with label c_epitope2 calculates somethingc_epitope4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope4
The COM action with label c_epitope4 calculates somethingc_epitope6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope6
The COM action with label c_epitope6 calculates somethingc_epitope8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope8
The COM action with label c_epitope8 calculates somethingc_epitope10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope10
The COM action with label c_epitope10 calculates somethingc_epitope12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope12
The COM action with label c_epitope12 calculates somethingc_epitope14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope14
The COM action with label c_epitope14 calculates somethingc_epitope16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope16
The COM action with label c_epitope16 calculates somethingc_epitope18: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope18
The COM action with label c_epitope18 calculates somethingc_epitope20: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope20
The COM action with label c_epitope20 calculates somethingc_epitope22: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=epitope22

# CV.1: Inter-tail contacts
The COM action with label c_epitope22 calculates somethingcon0: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con0 calculates the following quantities:
 Quantity   
 Description  
con0.value
the value of the coordinationcon1: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con1 calculates the following quantities:
 Quantity   
 Description  
con1.value
the value of the coordinationcon2: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con2 calculates the following quantities:
 Quantity   
 Description  
con2.value
the value of the coordinationcon3: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con3 calculates the following quantities:
 Quantity   
 Description  
con3.value
the value of the coordinationcon4: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con4 calculates the following quantities:
 Quantity   
 Description  
con4.value
the value of the coordinationcon5: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con5 calculates the following quantities:
 Quantity   
 Description  
con5.value
the value of the coordinationcon6: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con6 calculates the following quantities:
 Quantity   
 Description  
con6.value
the value of the coordinationcon7: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con7 calculates the following quantities:
 Quantity   
 Description  
con7.value
the value of the coordinationcon8: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con8 calculates the following quantities:
 Quantity   
 Description  
con8.value
the value of the coordinationcon9: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label con9 calculates the following quantities:
 Quantity   
 Description  
con9.value
the value of the coordinationcon10: COORDINATIONCalculate coordination numbers. 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 COM of tials and epitopes
The COORDINATION action with label con10 calculates the following quantities:
 Quantity   
 Description  
con10.value
the value of the coordinationdcm_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
The DISTANCE action with label dcm_0 calculates the following quantities:
 Quantity   
 Description  
dcm_0.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_2 calculates the following quantities:
 Quantity   
 Description  
dcm_2.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_4 calculates the following quantities:
 Quantity   
 Description  
dcm_4.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_6 calculates the following quantities:
 Quantity   
 Description  
dcm_6.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_8 calculates the following quantities:
 Quantity   
 Description  
dcm_8.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_10 calculates the following quantities:
 Quantity   
 Description  
dcm_10.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_12 calculates the following quantities:
 Quantity   
 Description  
dcm_12.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_14 calculates the following quantities:
 Quantity   
 Description  
dcm_14.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_16 calculates the following quantities:
 Quantity   
 Description  
dcm_16.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_18 calculates the following quantities:
 Quantity   
 Description  
dcm_18.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_20 calculates the following quantities:
 Quantity   
 Description  
dcm_20.value
the DISTANCE between this pair of atomsdcm_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
The DISTANCE action with label dcm_22 calculates the following quantities:
 Quantity   
 Description  
dcm_22.value
the DISTANCE between this pair of atomsalpha0: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha0 calculates the following quantities:
 Quantity   
 Description  
alpha0.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha0.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha0.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha2: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha2 calculates the following quantities:
 Quantity   
 Description  
alpha2.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha4: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha4 calculates the following quantities:
 Quantity   
 Description  
alpha4.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha4.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha4.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha6: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha6 calculates the following quantities:
 Quantity   
 Description  
alpha6.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha8: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha8 calculates the following quantities:
 Quantity   
 Description  
alpha8.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha8.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha8.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha10: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha10 calculates the following quantities:
 Quantity   
 Description  
alpha10.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha10.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha10.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha14: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha14 calculates the following quantities:
 Quantity   
 Description  
alpha14.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha14.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha14.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha12: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha12 calculates the following quantities:
 Quantity   
 Description  
alpha12.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha12.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha12.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha16: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha16 calculates the following quantities:
 Quantity   
 Description  
alpha16.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha16.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha16.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha18: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha18 calculates the following quantities:
 Quantity   
 Description  
alpha18.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha18.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha18.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha20: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha20 calculates the following quantities:
 Quantity   
 Description  
alpha20.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha20.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha20.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdalpha22: ALPHARMSDProbe the alpha helical content of a protein structure. 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
The ALPHARMSD action with label alpha22 calculates the following quantities:
 Quantity   
 Description  
alpha22.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
alpha22.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha22.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdMOLINFOThis 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
parabeta0: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta0 calculates the following quantities:
 Quantity   
 Description  
parabeta0.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta0.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta0.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta2: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta2 calculates the following quantities:
 Quantity   
 Description  
parabeta2.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta4: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta4 calculates the following quantities:
 Quantity   
 Description  
parabeta4.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta4.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta4.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta6: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta6 calculates the following quantities:
 Quantity   
 Description  
parabeta6.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta8: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta8 calculates the following quantities:
 Quantity   
 Description  
parabeta8.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta8.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta8.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta10: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta10 calculates the following quantities:
 Quantity   
 Description  
parabeta10.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta10.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta10.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta12: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta12 calculates the following quantities:
 Quantity   
 Description  
parabeta12.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta12.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta12.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta14: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta14 calculates the following quantities:
 Quantity   
 Description  
parabeta14.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta14.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta14.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta16: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta16 calculates the following quantities:
 Quantity   
 Description  
parabeta16.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta16.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta16.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta18: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta18 calculates the following quantities:
 Quantity   
 Description  
parabeta18.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta18.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta18.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta20: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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
The PARABETARMSD action with label parabeta20 calculates the following quantities:
 Quantity   
 Description  
parabeta20.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta20.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta20.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdparabeta22: PARABETARMSDProbe the parallel beta sheet content of your protein structure. 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

The PARABETARMSD action with label parabeta22 calculates the following quantities:
 Quantity   
 Description  
parabeta22.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
parabeta22.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
parabeta22.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdPBMETADUsed 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=200 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
...

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potentialEMMICalculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details ...
ARGthe labels of the values from which the function is calculated=pb.bias REWEIGHT simple REWEIGHT using the ARG as energy
LABELa label for the action so that its output can be referenced in the input to other actions=gmm NOPBC ignore the periodic boundary conditions when calculating distances TEMPtemperature=310.0 NL_STRIDEThe frequency with which we are updating the neighbor list=100 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01
ATOMSatoms for which we calculate the density map, typically all heavy atoms=Protein-noASPGLU-noH GMM_FILEfile with the parameters of the GMM components=map.dat
#the larger the number the softer the contribution of the EM data
SIGMA0initial value of the uncertainty=5.0 SIGMA_MINminimum uncertainty=0.05 DSIGMAMC step for uncertainties=0.1 RESOLUTIONCryo-EM map resolution=0.25 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=GAUSS
OPTSIGMAMEAN SIGMA_MEAN0=2.0
AVERAGINGAveraging window for weights=200 WRITE_STRIDEwrite the status to a file every N steps, this can be used for restart=10000
...

# translate into bias
The EMMI action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.acc
MC acceptance for uncertainty
gmm.weight
weights of the weighted average
gmm.biasDer
derivatives with respect to the bias
gmm.sigma
uncertainty in the forward models and experiment
gmm.neff
effective number of replicasemr: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=gmm.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=2

# print useful info to file
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint 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=5000