PLUMED-NEST-TEST-SITE

Project ID: plumID:22.023
Source: ANALYSIS/plumed_analysis.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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingMOLINFOThis 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
protein-h: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
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

The TORSION action with label disulf8 calculates the following quantities:
 Quantity   
 Description  
disulf8.value
the TORSION involving these atomsph1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-223the four atoms that are required to calculate the phi dihedral for residue 223. Click here for more information. 
The TORSION action with label ph1 calculates the following quantities:
 Quantity   
 Description  
ph1.value
the TORSION involving these atomsph2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-224the four atoms that are required to calculate the phi dihedral for residue 224. Click here for more information. 
The TORSION action with label ph2 calculates the following quantities:
 Quantity   
 Description  
ph2.value
the TORSION involving these atomsph3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-225the four atoms that are required to calculate the phi dihedral for residue 225. Click here for more information. 
The TORSION action with label ph3 calculates the following quantities:
 Quantity   
 Description  
ph3.value
the TORSION involving these atomsph4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-226the four atoms that are required to calculate the phi dihedral for residue 226. Click here for more information. 
The TORSION action with label ph4 calculates the following quantities:
 Quantity   
 Description  
ph4.value
the TORSION involving these atomsph5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-227the four atoms that are required to calculate the phi dihedral for residue 227. Click here for more information. 
The TORSION action with label ph5 calculates the following quantities:
 Quantity   
 Description  
ph5.value
the TORSION involving these atomsph6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-228the four atoms that are required to calculate the phi dihedral for residue 228. Click here for more information. 
The TORSION action with label ph6 calculates the following quantities:
 Quantity   
 Description  
ph6.value
the TORSION involving these atomsph7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-229the four atoms that are required to calculate the phi dihedral for residue 229. Click here for more information. 
The TORSION action with label ph7 calculates the following quantities:
 Quantity   
 Description  
ph7.value
the TORSION involving these atomsph8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-230the four atoms that are required to calculate the phi dihedral for residue 230. Click here for more information. 
The TORSION action with label ph8 calculates the following quantities:
 Quantity   
 Description  
ph8.value
the TORSION involving these atomsph9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-231the four atoms that are required to calculate the phi dihedral for residue 231. Click here for more information. 
The TORSION action with label ph9 calculates the following quantities:
 Quantity   
 Description  
ph9.value
the TORSION involving these atomsph10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-232the four atoms that are required to calculate the phi dihedral for residue 232. Click here for more information. 
The TORSION action with label ph10 calculates the following quantities:
 Quantity   
 Description  
ph10.value
the TORSION involving these atomsph11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-233the four atoms that are required to calculate the phi dihedral for residue 233. Click here for more information. 
The TORSION action with label ph11 calculates the following quantities:
 Quantity   
 Description  
ph11.value
the TORSION involving these atomsph12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-234the four atoms that are required to calculate the phi dihedral for residue 234. Click here for more information. 


The TORSION action with label ph12 calculates the following quantities:
 Quantity   
 Description  
ph12.value
the TORSION involving these atomsps1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-223the four atoms that are required to calculate the psi dihedral for residue 223. Click here for more information. 
The TORSION action with label ps1 calculates the following quantities:
 Quantity   
 Description  
ps1.value
the TORSION involving these atomsps2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-224the four atoms that are required to calculate the psi dihedral for residue 224. Click here for more information. 
The TORSION action with label ps2 calculates the following quantities:
 Quantity   
 Description  
ps2.value
the TORSION involving these atomsps3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-225the four atoms that are required to calculate the psi dihedral for residue 225. Click here for more information. 
The TORSION action with label ps3 calculates the following quantities:
 Quantity   
 Description  
ps3.value
the TORSION involving these atomsps4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-226the four atoms that are required to calculate the psi dihedral for residue 226. Click here for more information. 
The TORSION action with label ps4 calculates the following quantities:
 Quantity   
 Description  
ps4.value
the TORSION involving these atomsps5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-227the four atoms that are required to calculate the psi dihedral for residue 227. Click here for more information. 
The TORSION action with label ps5 calculates the following quantities:
 Quantity   
 Description  
ps5.value
the TORSION involving these atomsps6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-228the four atoms that are required to calculate the psi dihedral for residue 228. Click here for more information. 
The TORSION action with label ps6 calculates the following quantities:
 Quantity   
 Description  
ps6.value
the TORSION involving these atomsps7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-229the four atoms that are required to calculate the psi dihedral for residue 229. Click here for more information. 
The TORSION action with label ps7 calculates the following quantities:
 Quantity   
 Description  
ps7.value
the TORSION involving these atomsps8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-230the four atoms that are required to calculate the psi dihedral for residue 230. Click here for more information. 
The TORSION action with label ps8 calculates the following quantities:
 Quantity   
 Description  
ps8.value
the TORSION involving these atomsps9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-231the four atoms that are required to calculate the psi dihedral for residue 231. Click here for more information. 
The TORSION action with label ps9 calculates the following quantities:
 Quantity   
 Description  
ps9.value
the TORSION involving these atomsps10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-232the four atoms that are required to calculate the psi dihedral for residue 232. Click here for more information. 
The TORSION action with label ps10 calculates the following quantities:
 Quantity   
 Description  
ps10.value
the TORSION involving these atomsps11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-233the four atoms that are required to calculate the psi dihedral for residue 233. Click here for more information. 
The TORSION action with label ps11 calculates the following quantities:
 Quantity   
 Description  
ps11.value
the TORSION involving these atomsps12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-234the four atoms that are required to calculate the psi dihedral for residue 234. Click here for more information. 


The TORSION action with label ps12 calculates the following quantities:
 Quantity   
 Description  
ps12.value
the TORSION involving these atomsph13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-297the four atoms that are required to calculate the phi dihedral for residue 297. Click here for more information. 
The TORSION action with label ph13 calculates the following quantities:
 Quantity   
 Description  
ph13.value
the TORSION involving these atomsph14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-299the four atoms that are required to calculate the phi dihedral for residue 299. Click here for more information. 
The TORSION action with label ph14 calculates the following quantities:
 Quantity   
 Description  
ph14.value
the TORSION involving these atomsph15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-299the four atoms that are required to calculate the phi dihedral for residue 299. Click here for more information. 
The TORSION action with label ph15 calculates the following quantities:
 Quantity   
 Description  
ph15.value
the TORSION involving these atomsph16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-300the four atoms that are required to calculate the phi dihedral for residue 300. Click here for more information. 
The TORSION action with label ph16 calculates the following quantities:
 Quantity   
 Description  
ph16.value
the TORSION involving these atomsph17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-301the four atoms that are required to calculate the phi dihedral for residue 301. Click here for more information. 
The TORSION action with label ph17 calculates the following quantities:
 Quantity   
 Description  
ph17.value
the TORSION involving these atomsph18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-302the four atoms that are required to calculate the phi dihedral for residue 302. Click here for more information. 
The TORSION action with label ph18 calculates the following quantities:
 Quantity   
 Description  
ph18.value
the TORSION involving these atomsph19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-303the four atoms that are required to calculate the phi dihedral for residue 303. Click here for more information. 
The TORSION action with label ph19 calculates the following quantities:
 Quantity   
 Description  
ph19.value
the TORSION involving these atomsph20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-304the four atoms that are required to calculate the phi dihedral for residue 304. Click here for more information. 
The TORSION action with label ph20 calculates the following quantities:
 Quantity   
 Description  
ph20.value
the TORSION involving these atomsph21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-305the four atoms that are required to calculate the phi dihedral for residue 305. Click here for more information. 
The TORSION action with label ph21 calculates the following quantities:
 Quantity   
 Description  
ph21.value
the TORSION involving these atomsph22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-306the four atoms that are required to calculate the phi dihedral for residue 306. Click here for more information. 
The TORSION action with label ph22 calculates the following quantities:
 Quantity   
 Description  
ph22.value
the TORSION involving these atomsph23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-307the four atoms that are required to calculate the phi dihedral for residue 307. Click here for more information. 
The TORSION action with label ph23 calculates the following quantities:
 Quantity   
 Description  
ph23.value
the TORSION involving these atomsph24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-308the four atoms that are required to calculate the phi dihedral for residue 308. Click here for more information. 


The TORSION action with label ph24 calculates the following quantities:
 Quantity   
 Description  
ph24.value
the TORSION involving these atomsps13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-297the four atoms that are required to calculate the psi dihedral for residue 297. Click here for more information. 
The TORSION action with label ps13 calculates the following quantities:
 Quantity   
 Description  
ps13.value
the TORSION involving these atomsps14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-299the four atoms that are required to calculate the psi dihedral for residue 299. Click here for more information. 
The TORSION action with label ps14 calculates the following quantities:
 Quantity   
 Description  
ps14.value
the TORSION involving these atomsps15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-299the four atoms that are required to calculate the psi dihedral for residue 299. Click here for more information. 
The TORSION action with label ps15 calculates the following quantities:
 Quantity   
 Description  
ps15.value
the TORSION involving these atomsps16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-300the four atoms that are required to calculate the psi dihedral for residue 300. Click here for more information. 
The TORSION action with label ps16 calculates the following quantities:
 Quantity   
 Description  
ps16.value
the TORSION involving these atomsps17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-301the four atoms that are required to calculate the psi dihedral for residue 301. Click here for more information. 
The TORSION action with label ps17 calculates the following quantities:
 Quantity   
 Description  
ps17.value
the TORSION involving these atomsps18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-302the four atoms that are required to calculate the psi dihedral for residue 302. Click here for more information. 
The TORSION action with label ps18 calculates the following quantities:
 Quantity   
 Description  
ps18.value
the TORSION involving these atomsps19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-303the four atoms that are required to calculate the psi dihedral for residue 303. Click here for more information. 
The TORSION action with label ps19 calculates the following quantities:
 Quantity   
 Description  
ps19.value
the TORSION involving these atomsps20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-304the four atoms that are required to calculate the psi dihedral for residue 304. Click here for more information. 
The TORSION action with label ps20 calculates the following quantities:
 Quantity   
 Description  
ps20.value
the TORSION involving these atomsps21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-305the four atoms that are required to calculate the psi dihedral for residue 305. Click here for more information. 
The TORSION action with label ps21 calculates the following quantities:
 Quantity   
 Description  
ps21.value
the TORSION involving these atomsps22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-306the four atoms that are required to calculate the psi dihedral for residue 306. Click here for more information. 
The TORSION action with label ps22 calculates the following quantities:
 Quantity   
 Description  
ps22.value
the TORSION involving these atomsps23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-307the four atoms that are required to calculate the psi dihedral for residue 307. Click here for more information. 
The TORSION action with label ps23 calculates the following quantities:
 Quantity   
 Description  
ps23.value
the TORSION involving these atomsps24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-308the four atoms that are required to calculate the psi dihedral for residue 308. Click here for more information. 


#UNBIASED
The TORSION action with label ps24 calculates the following quantities:
 Quantity   
 Description  
ps24.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 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 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 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 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 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 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 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


#UNBIASED Tail definitions
The GROUP action with label tail15 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 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 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 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 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 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 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 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 atomsPBMETADUsed to performed Parallel Bias metadynamics. More details ...
    # Carlo's Biasfactor rule-of-thumb: 10 * sqrt(number of CVs)
    BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=56 HEIGHTthe height of the Gaussian hills, one for all biases=0.3 PACEthe frequency for hill addition, one for all biases=500000000 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR LABELa label for the action so that its output can be referenced in the input to other actions=pb GRID_WSTRIDEfrequency for dumping the grid=10000 SIGMAthe widths of the Gaussian hills=1000 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
    ARGthe labels of the scalars on which the bias will act=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7
    SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.5,0.5,0.5,0.5,0.5,0.5,0.5
    SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,20,20,20,20,20,20,20
    GRID_MINthe lower bounds for the grid=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0,0,0,0,0,0,0
    GRID_MAXthe upper bounds for the grid=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,3820,3820,3820,3820,3820,3820,3820
    FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=thomas_marco/HILLS_disulf1,thomas_marco/HILLS_disulf2,thomas_marco/HILLS_disulf3,thomas_marco/HILLS_disulf4,thomas_marco/HILLS_disulf5,thomas_marco/HILLS_disulf6,thomas_marco/HILLS_disulf7,thomas_marco/HILLS_disulf8,thomas_marco/HILLS_tor1,thomas_marco/HILLS_tor2,thomas_marco/HILLS_tor3,thomas_marco/HILLS_tor4,thomas_marco/HILLS_tor5,thomas_marco/HILLS_tor6,thomas_marco/HILLS_tor7,thomas_marco/HILLS_tor8,thomas_marco/HILLS_con1,thomas_marco/HILLS_con2,thomas_marco/HILLS_con3,thomas_marco/HILLS_con4,thomas_marco/HILLS_con5,thomas_marco/HILLS_con6,thomas_marco/HILLS_con7
    GRID_RFILESread grid for the bias=thomas_marco/GRID_disulf1,thomas_marco/GRID_disulf2,thomas_marco/GRID_disulf3,thomas_marco/GRID_disulf4,thomas_marco/GRID_disulf5,thomas_marco/GRID_disulf6,thomas_marco/GRID_disulf7,thomas_marco/GRID_disulf8,thomas_marco/GRID_tor1,thomas_marco/GRID_tor2,thomas_marco/GRID_tor3,thomas_marco/GRID_tor4,thomas_marco/GRID_tor5,thomas_marco/GRID_tor6,thomas_marco/GRID_tor7,thomas_marco/GRID_tor8,thomas_marco/GRID_con1,thomas_marco/GRID_con2,thomas_marco/GRID_con3,thomas_marco/GRID_con4,thomas_marco/GRID_con5,thomas_marco/GRID_con6,thomas_marco/GRID_con7
    GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=thomas_marco/GRID_disulf1,thomas_marco/GRID_disulf2,thomas_marco/GRID_disulf3,thomas_marco/GRID_disulf4,thomas_marco/GRID_disulf5,thomas_marco/GRID_disulf6,thomas_marco/GRID_disulf7,thomas_marco/GRID_disulf8,thomas_marco/GRID_tor1,thomas_marco/GRID_tor2,thomas_marco/GRID_tor3,thomas_marco/GRID_tor4,thomas_marco/GRID_tor5,thomas_marco/GRID_tor6,thomas_marco/GRID_tor7,thomas_marco/GRID_tor8,thomas_marco/GRID_con1,thomas_marco/GRID_con2,thomas_marco/GRID_con3,thomas_marco/GRID_con4,thomas_marco/GRID_con5,thomas_marco/GRID_con6,thomas_marco/GRID_con7
    TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310
...

#EMMI ...
#    ARG=pb.bias REWEIGHT
#    LABEL=gmm NOPBC TEMP=310.0 NL_STRIDE=100 NL_CUTOFF=0.01
#    ATOMS=protein-h GMM_FILE=../iapp.dat
#    # the larger the number the softer the contribution of the EM data
#    SIGMA0=5.0 SIGMA_MIN=0.05 DSIGMA=0.1 RESOLUTION=0.1 NOISETYPE=GAUSS
#    OPTSIGMAMEAN SIGMA_MEAN0=2.0
#    AVERAGING=200 WRITE_STRIDE=10000
#...

# translate into bias
#emr: BIASVALUE ARG=gmm.scoreb STRIDE=2

# print useful info to file
#PRINT ARG=gmm.* FILE=EMMI STRIDE=500

#PRINT ARG=pb.bias FILE=FULLBIAS
#PRINT ARG=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7,pb.bias FILE=COLVAR STRIDE=1
#PRINT ARG=disulf9,disulf10,disulf11,disulf12,disulf13,disulf14,disulf15,disulf16,tor9,tor10,tor11,tor12,tor13,tor14,tor15,tor16,con8,con9,con10,con11,con12,con13,con14 FILE=COLVAR_UNBIASED STRIDE=1

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7,pb.bias,ph1,ph2,ph3,ph4,ph5,ph6,ph7,ph8,ph9,ph10,ph11,ph12,ph13,ph14,ph15,ph16,ph17,ph18,ph19,ph20,ph21,ph22,ph23,ph24,ps1,ps2,ps3,ps4,ps5,ps6,ps7,ps8,ps9,ps10,ps11,ps12,ps13,ps14,ps15,ps16,ps17,ps18,ps19,ps20,ps21,ps22,ps23,ps24 FILEthe name of the file on which to output these quantities=COLVAR_r3r4 STRIDE the frequency with which the quantities of interest should be output=1