PLUMED-NEST-TEST-SITE

Project ID: plumID:22.023
Source: ANALYSIS/plumed_analysis_unbiased.dat
Originally used with PLUMED version: 2.6-mod
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.pdb

# define all heavy atoms using GROMACS index file
The MOLINFO action with label  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: 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
The GROUP action with label protein 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

# make protein whole: add reference position of first heavy atom (in nm)
The GROUP action with label system calculates somethingWHOLEMOLECULESThis 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=1-537 ENTITY1the atoms that make up a molecule that you wish to align=538-1074 ENTITY2the atoms that make up a molecule that you wish to align=1075-1611 ENTITY3the atoms that make up a molecule that you wish to align=1612-2148 ENTITY4the atoms that make up a molecule that you wish to align=2149-2685 ENTITY5the atoms that make up a molecule that you wish to align=2686-3222 ENTITY6the atoms that make up a molecule that you wish to align=3223-3759 ENTITY7the atoms that make up a molecule that you wish to align=3760-4296 ENTITY8the atoms that make up a molecule that you wish to align=4297-4833 ENTITY9the atoms that make up a molecule that you wish to align=4834-5370 ENTITY10the atoms that make up a molecule that you wish to align=5371-5907 ENTITY11the atoms that make up a molecule that you wish to align=5908-6444 ENTITY12the atoms that make up a molecule that you wish to align=6445-6981 ENTITY13the atoms that make up a molecule that you wish to align=6982-7518 ENTITY14the atoms that make up a molecule that you wish to align=7519-8055 ENTITY15the atoms that make up a molecule that you wish to align=8056-8592 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file REF0=7.977,12.295,6.939 REF1=11.453,6.771,7.163 REF2=7.857,12.19,7.532 REF3=11.438,6.79,7.776 REF4=7.661,12.18,8.36 REF5=11.474,6.687,8.62 REF6=7.569,12.049,8.69   REF7=11.475,6.772,8.977 REF8=7.658,11.999,9.265 REF9=11.274,6.704,9.522  REF10=7.191,11.806,9.51 REF11=11.639,6.928,9.885 REF12=7.515,11.723,10.332 REF13=11.16,6.807,10.622 REF14=7.347,11.62,10.843 REF15=11.207,6.847,11.166

# Constrain the protein CA protofibril core
RMSDCalculate 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=fibril_core.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 

# Disulfide dihedral (CYS2:CB,CYS2:S,CYS7:S,CYS7:CB)
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 potentialdisulf1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=29,32,94,91
The TORSION action with label disulf1 calculates the following quantities:
 Quantity   
 Description  
disulf1.value
the TORSION involving these atomsdisulf2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1103,1106,1168,1165
The TORSION action with label disulf2 calculates the following quantities:
 Quantity   
 Description  
disulf2.value
the TORSION involving these atomsdisulf3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2177,2180,2242,2239
The TORSION action with label disulf3 calculates the following quantities:
 Quantity   
 Description  
disulf3.value
the TORSION involving these atomsdisulf4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3251,3254,3316,3313
The TORSION action with label disulf4 calculates the following quantities:
 Quantity   
 Description  
disulf4.value
the TORSION involving these atomsdisulf5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4325,4328,4390,4387
The TORSION action with label disulf5 calculates the following quantities:
 Quantity   
 Description  
disulf5.value
the TORSION involving these atomsdisulf6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5399,5402,5464,5461
The TORSION action with label disulf6 calculates the following quantities:
 Quantity   
 Description  
disulf6.value
the TORSION involving these atomsdisulf7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=6473,6476,6538,6535
The TORSION action with label disulf7 calculates the following quantities:
 Quantity   
 Description  
disulf7.value
the TORSION involving these atomsdisulf8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7547,7550,7612,7609

#UNBIASED
The TORSION action with label disulf8 calculates the following quantities:
 Quantity   
 Description  
disulf8.value
the TORSION involving these atomsdisulf9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=566,569,631,628
The TORSION action with label disulf9 calculates the following quantities:
 Quantity   
 Description  
disulf9.value
the TORSION involving these atomsdisulf10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1640,1643,1705,1702
The TORSION action with label disulf10 calculates the following quantities:
 Quantity   
 Description  
disulf10.value
the TORSION involving these atomsdisulf11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2714,2717,2779,2776
The TORSION action with label disulf11 calculates the following quantities:
 Quantity   
 Description  
disulf11.value
the TORSION involving these atomsdisulf12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3788,3791,3853,3850
The TORSION action with label disulf12 calculates the following quantities:
 Quantity   
 Description  
disulf12.value
the TORSION involving these atomsdisulf13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4862,4865,4927,4924
The TORSION action with label disulf13 calculates the following quantities:
 Quantity   
 Description  
disulf13.value
the TORSION involving these atomsdisulf14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5936,5939,6001,5998
The TORSION action with label disulf14 calculates the following quantities:
 Quantity   
 Description  
disulf14.value
the TORSION involving these atomsdisulf15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7010,7013,7075,7072
The TORSION action with label disulf15 calculates the following quantities:
 Quantity   
 Description  
disulf15.value
the TORSION involving these atomsdisulf16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8084,8087,8149,8146
###############################

# Tail definitions
The TORSION action with label disulf16 calculates the following quantities:
 Quantity   
 Description  
disulf16.value
the TORSION involving these atomstail1: 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=tail1
The GROUP action with label tail1 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 somethingtail3: 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=tail3
The GROUP action with label tail3 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 somethingtail5: 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=tail5
The GROUP action with label tail5 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 somethingtail7: 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=tail7
The GROUP action with label tail7 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 somethingtail9: 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=tail9
The GROUP action with label tail9 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 somethingtail11: 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=tail11
The GROUP action with label tail11 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 somethingtail13: 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=tail13
The GROUP action with label tail13 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 somethingtail15: 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=tail15
The GROUP action with label tail15 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


# Inter-tail contacts
# Theoretical maximum: 3828
The GROUP action with label tail16 calculates somethingcon1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=tail1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail3 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=tail3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail5 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=tail5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail7 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=tail7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail9 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=tail9 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail11 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=tail11 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail13 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=tail13 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=tail15 R_0The r_0 parameter of the switching function=0.8

#UNBIASED
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=tail2 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 con8 calculates the following quantities:
 Quantity   
 Description  
con8.value
the value of the coordinationcon9: 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)=tail6 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=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 con10 calculates the following quantities:
 Quantity   
 Description  
con10.value
the value of the coordinationcon11: 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)=tail10 R_0The r_0 parameter of the switching function=0.8
The COORDINATION action with label con11 calculates the following quantities:
 Quantity   
 Description  
con11.value
the value of the coordinationcon12: 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 con12 calculates the following quantities:
 Quantity   
 Description  
con12.value
the value of the coordinationcon13: 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)=tail14 R_0The r_0 parameter of the switching function=0.8
The COORDINATION action with label con13 calculates the following quantities:
 Quantity   
 Description  
con13.value
the value of the coordinationcon14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=tail14 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
#################

# 1
The COORDINATION action with label con14 calculates the following quantities:
 Quantity   
 Description  
con14.value
the value of the coordinationcom-cys2-1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-2the protein/dna/rna backbone atoms in residue 2. Click here for more information. 
The COM action with label com-cys2-1 calculates somethingcom-cys7-1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-7the protein/dna/rna backbone atoms in residue 7. Click here for more information. 
The COM action with label com-cys7-1 calculates somethingcom-as14-1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-14the protein/dna/rna backbone atoms in residue 14. Click here for more information. 
The COM action with label com-as14-1 calculates somethingcom-as31-1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-31the protein/dna/rna backbone atoms in residue 31. Click here for more information. 
# 2
The COM action with label com-as31-1 calculates somethingcom-cys2-2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-76the protein/dna/rna backbone atoms in residue 76. Click here for more information. 
The COM action with label com-cys2-2 calculates somethingcom-cys7-2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-81the protein/dna/rna backbone atoms in residue 81. Click here for more information. 
The COM action with label com-cys7-2 calculates somethingcom-as14-2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-88the protein/dna/rna backbone atoms in residue 88. Click here for more information. 
The COM action with label com-as14-2 calculates somethingcom-as31-2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-105the protein/dna/rna backbone atoms in residue 105. Click here for more information. 
# 3
The COM action with label com-as31-2 calculates somethingcom-cys2-3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-150the protein/dna/rna backbone atoms in residue 150. Click here for more information. 
The COM action with label com-cys2-3 calculates somethingcom-cys7-3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-155the protein/dna/rna backbone atoms in residue 155. Click here for more information. 
The COM action with label com-cys7-3 calculates somethingcom-as14-3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-162the protein/dna/rna backbone atoms in residue 162. Click here for more information. 
The COM action with label com-as14-3 calculates somethingcom-as31-3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-179the protein/dna/rna backbone atoms in residue 179. Click here for more information. 
# 4
The COM action with label com-as31-3 calculates somethingcom-cys2-4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-224the protein/dna/rna backbone atoms in residue 224. Click here for more information. 
The COM action with label com-cys2-4 calculates somethingcom-cys7-4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-229the protein/dna/rna backbone atoms in residue 229. Click here for more information. 
The COM action with label com-cys7-4 calculates somethingcom-as14-4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-236the protein/dna/rna backbone atoms in residue 236. Click here for more information. 
The COM action with label com-as14-4 calculates somethingcom-as31-4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-253the protein/dna/rna backbone atoms in residue 253. Click here for more information. 
# 5
The COM action with label com-as31-4 calculates somethingcom-cys2-5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-298the protein/dna/rna backbone atoms in residue 298. Click here for more information. 
The COM action with label com-cys2-5 calculates somethingcom-cys7-5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-303the protein/dna/rna backbone atoms in residue 303. Click here for more information. 
The COM action with label com-cys7-5 calculates somethingcom-as14-5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-310the protein/dna/rna backbone atoms in residue 310. Click here for more information. 
The COM action with label com-as14-5 calculates somethingcom-as31-5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-327the protein/dna/rna backbone atoms in residue 327. Click here for more information. 
# 6
The COM action with label com-as31-5 calculates somethingcom-cys2-6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-372the protein/dna/rna backbone atoms in residue 372. Click here for more information. 
The COM action with label com-cys2-6 calculates somethingcom-cys7-6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-377the protein/dna/rna backbone atoms in residue 377. Click here for more information. 
The COM action with label com-cys7-6 calculates somethingcom-as14-6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-384the protein/dna/rna backbone atoms in residue 384. Click here for more information. 
The COM action with label com-as14-6 calculates somethingcom-as31-6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-401the protein/dna/rna backbone atoms in residue 401. Click here for more information. 
# 7
The COM action with label com-as31-6 calculates somethingcom-cys2-7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-446the protein/dna/rna backbone atoms in residue 446. Click here for more information. 
The COM action with label com-cys2-7 calculates somethingcom-cys7-7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-451the protein/dna/rna backbone atoms in residue 451. Click here for more information. 
The COM action with label com-cys7-7 calculates somethingcom-as14-7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-458the protein/dna/rna backbone atoms in residue 458. Click here for more information. 
The COM action with label com-as14-7 calculates somethingcom-as31-7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-475the protein/dna/rna backbone atoms in residue 475. Click here for more information. 
# 8
The COM action with label com-as31-7 calculates somethingcom-cys2-8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-520the protein/dna/rna backbone atoms in residue 520. Click here for more information. 
The COM action with label com-cys2-8 calculates somethingcom-cys7-8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-525the protein/dna/rna backbone atoms in residue 525. Click here for more information. 
The COM action with label com-cys7-8 calculates somethingcom-as14-8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-532the protein/dna/rna backbone atoms in residue 532. Click here for more information. 
The COM action with label com-as14-8 calculates somethingcom-as31-8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-549the protein/dna/rna backbone atoms in residue 549. Click here for more information. 

# Tail torsion (CYS2:CA,CYS7:CA,ASN14:CA,ASN31:CA)
The COM action with label com-as31-8 calculates somethingtor1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-1,com-cys7-1,com-as14-1,com-as31-1
The TORSION action with label tor1 calculates the following quantities:
 Quantity   
 Description  
tor1.value
the TORSION involving these atomstor2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-2,com-cys7-2,com-as14-2,com-as31-2
The TORSION action with label tor2 calculates the following quantities:
 Quantity   
 Description  
tor2.value
the TORSION involving these atomstor3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-3,com-cys7-3,com-as14-3,com-as31-3
The TORSION action with label tor3 calculates the following quantities:
 Quantity   
 Description  
tor3.value
the TORSION involving these atomstor4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-4,com-cys7-4,com-as14-4,com-as31-4
The TORSION action with label tor4 calculates the following quantities:
 Quantity   
 Description  
tor4.value
the TORSION involving these atomstor5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-5,com-cys7-5,com-as14-5,com-as31-5
The TORSION action with label tor5 calculates the following quantities:
 Quantity   
 Description  
tor5.value
the TORSION involving these atomstor6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-6,com-cys7-6,com-as14-6,com-as31-6
The TORSION action with label tor6 calculates the following quantities:
 Quantity   
 Description  
tor6.value
the TORSION involving these atomstor7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-7,com-cys7-7,com-as14-7,com-as31-7
The TORSION action with label tor7 calculates the following quantities:
 Quantity   
 Description  
tor7.value
the TORSION involving these atomstor8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-8,com-cys7-8,com-as14-8,com-as31-8

#UNBIASED
# 1
The TORSION action with label tor8 calculates the following quantities:
 Quantity   
 Description  
tor8.value
the TORSION involving these atomscom-cys2-9: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-39the protein/dna/rna backbone atoms in residue 39. Click here for more information. 
The COM action with label com-cys2-9 calculates somethingcom-cys7-9: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-44the protein/dna/rna backbone atoms in residue 44. Click here for more information. 
The COM action with label com-cys7-9 calculates somethingcom-as14-9: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-51the protein/dna/rna backbone atoms in residue 51. Click here for more information. 
The COM action with label com-as14-9 calculates somethingcom-as31-9: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-68the protein/dna/rna backbone atoms in residue 68. Click here for more information. 
# 2
The COM action with label com-as31-9 calculates somethingcom-cys2-10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-113the protein/dna/rna backbone atoms in residue 113. Click here for more information. 
The COM action with label com-cys2-10 calculates somethingcom-cys7-10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-118the protein/dna/rna backbone atoms in residue 118. Click here for more information. 
The COM action with label com-cys7-10 calculates somethingcom-as14-10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-125the protein/dna/rna backbone atoms in residue 125. Click here for more information. 
The COM action with label com-as14-10 calculates somethingcom-as31-10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-142the protein/dna/rna backbone atoms in residue 142. Click here for more information. 
# 3                          
The COM action with label com-as31-10 calculates somethingcom-cys2-11: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-187the protein/dna/rna backbone atoms in residue 187. Click here for more information. 
The COM action with label com-cys2-11 calculates somethingcom-cys7-11: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-192the protein/dna/rna backbone atoms in residue 192. Click here for more information. 
The COM action with label com-cys7-11 calculates somethingcom-as14-11: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-199the protein/dna/rna backbone atoms in residue 199. Click here for more information. 
The COM action with label com-as14-11 calculates somethingcom-as31-11: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-216the protein/dna/rna backbone atoms in residue 216. Click here for more information. 
# 4                          
The COM action with label com-as31-11 calculates somethingcom-cys2-12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-261the protein/dna/rna backbone atoms in residue 261. Click here for more information. 
The COM action with label com-cys2-12 calculates somethingcom-cys7-12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-266the protein/dna/rna backbone atoms in residue 266. Click here for more information. 
The COM action with label com-cys7-12 calculates somethingcom-as14-12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-273the protein/dna/rna backbone atoms in residue 273. Click here for more information. 
The COM action with label com-as14-12 calculates somethingcom-as31-12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-290the protein/dna/rna backbone atoms in residue 290. Click here for more information. 
# 5                          
The COM action with label com-as31-12 calculates somethingcom-cys2-13: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-335the protein/dna/rna backbone atoms in residue 335. Click here for more information. 
The COM action with label com-cys2-13 calculates somethingcom-cys7-13: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-340the protein/dna/rna backbone atoms in residue 340. Click here for more information. 
The COM action with label com-cys7-13 calculates somethingcom-as14-13: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-347the protein/dna/rna backbone atoms in residue 347. Click here for more information. 
The COM action with label com-as14-13 calculates somethingcom-as31-13: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-364the protein/dna/rna backbone atoms in residue 364. Click here for more information. 
# 6                          
The COM action with label com-as31-13 calculates somethingcom-cys2-14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-409the protein/dna/rna backbone atoms in residue 409. Click here for more information. 
The COM action with label com-cys2-14 calculates somethingcom-cys7-14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-414the protein/dna/rna backbone atoms in residue 414. Click here for more information. 
The COM action with label com-cys7-14 calculates somethingcom-as14-14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-421the protein/dna/rna backbone atoms in residue 421. Click here for more information. 
The COM action with label com-as14-14 calculates somethingcom-as31-14: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-438the protein/dna/rna backbone atoms in residue 438. Click here for more information. 
# 7                          
The COM action with label com-as31-14 calculates somethingcom-cys2-15: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-483the protein/dna/rna backbone atoms in residue 483. Click here for more information. 
The COM action with label com-cys2-15 calculates somethingcom-cys7-15: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-488the protein/dna/rna backbone atoms in residue 488. Click here for more information. 
The COM action with label com-cys7-15 calculates somethingcom-as14-15: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-495the protein/dna/rna backbone atoms in residue 495. Click here for more information. 
The COM action with label com-as14-15 calculates somethingcom-as31-15: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-512the protein/dna/rna backbone atoms in residue 512. Click here for more information. 
# 8                          
The COM action with label com-as31-15 calculates somethingcom-cys2-16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-557the protein/dna/rna backbone atoms in residue 557. Click here for more information. 
The COM action with label com-cys2-16 calculates somethingcom-cys7-16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-562the protein/dna/rna backbone atoms in residue 562. Click here for more information. 
The COM action with label com-cys7-16 calculates somethingcom-as14-16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-569the protein/dna/rna backbone atoms in residue 569. Click here for more information. 
The COM action with label com-as14-16 calculates somethingcom-as31-16: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=@back-586the protein/dna/rna backbone atoms in residue 586. Click here for more information. 

# Tail torsion (CYS2:CA,CYS7:CA,ASN14:CA,ASN31:CA)
The COM action with label com-as31-16 calculates somethingtor9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-9,com-cys7-9,com-as14-9,com-as31-9
The TORSION action with label tor9 calculates the following quantities:
 Quantity   
 Description  
tor9.value
the TORSION involving these atomstor10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-10,com-cys7-10,com-as14-10,com-as31-10
The TORSION action with label tor10 calculates the following quantities:
 Quantity   
 Description  
tor10.value
the TORSION involving these atomstor11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-11,com-cys7-11,com-as14-11,com-as31-11
The TORSION action with label tor11 calculates the following quantities:
 Quantity   
 Description  
tor11.value
the TORSION involving these atomstor12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-12,com-cys7-12,com-as14-12,com-as31-12
The TORSION action with label tor12 calculates the following quantities:
 Quantity   
 Description  
tor12.value
the TORSION involving these atomstor13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-13,com-cys7-13,com-as14-13,com-as31-13
The TORSION action with label tor13 calculates the following quantities:
 Quantity   
 Description  
tor13.value
the TORSION involving these atomstor14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-14,com-cys7-14,com-as14-14,com-as31-14
The TORSION action with label tor14 calculates the following quantities:
 Quantity   
 Description  
tor14.value
the TORSION involving these atomstor15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-15,com-cys7-15,com-as14-15,com-as31-15
The TORSION action with label tor15 calculates the following quantities:
 Quantity   
 Description  
tor15.value
the TORSION involving these atomstor16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com-cys2-16,com-cys7-16,com-as14-16,com-as31-16
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The TORSION action with label tor16 calculates the following quantities:
 Quantity   
 Description  
tor16.value
the TORSION involving these atomsPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=disulf9,disulf10,disulf11,disulf12,disulf13,disulf14,disulf15,disulf16,tor9,tor10,tor11,tor12,tor13,tor14,tor15,tor16,con8,con9,con10,con11,con12,con13,con14 FILEthe name of the file on which to output these quantities=COLVAR_UNBIASED STRIDE the frequency with which the quantities of interest should be output=1