PLUMED-NEST

Project ID: plumID:20.014
Source: PLUMED_input_files/AB42_and_10074_G5/plumed/plumed.dat
Originally used with PLUMED version: 2.6.0
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

#SETTINGS NREPLICAS=2
#this is the master plumed.dat file for metadynamic metainference simulations

# define groups
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=../system/template.pdb
The MOLINFO action with label  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=1-627 ENTITY1the atoms that make up a molecule that you wish to align=628-664
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000

#include file with definition of metadynamics CVs on peptide
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=CVs.dat
# The command:
# INCLUDE FILE=CVs.dat
# ensures PLUMED loads the contents of the file called CVs.dat
# The contents of this file are shown below (click the red comment to hide them).
#This is the metadynamics CV file for CVs on the peptide

#CV1 alpha helix
The INCLUDE action with label CVs.dat calculates somethingALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-42 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=helix

#CV2 sum parallel and anti-parallel beta-content
The ALPHARMSD action with label helix calculates the following quantities:
 Quantity   
 Description  
helix.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
helix.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
helix.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdPARABETARMSDProbe the parallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-42 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=par
The PARABETARMSD action with label par calculates the following quantities:
 Quantity   
 Description  
par.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet
par.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
par.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-42 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=anti
The ANTIBETARMSD action with label anti calculates the following quantities:
 Quantity   
 Description  
anti.value
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet
anti.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=par.lessthan,anti.lessthan PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=beta

#CV3 radius of gyration
The COMBINE action with label beta calculates the following quantities:
 Quantity   
 Description  
beta.value
a linear compbinationca: 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 ATOMSthe numerical indexes for the set of atoms in the group=5,17,27,42,62,86,103,115,126,133,154,169,185,202,219,236,258,277,293,313,333,343,358,370,386,393,404,418,440,447,457,476,495,502,521,538,554,561,568,584,600,619
The GROUP action with label ca calculates somethingrgyr: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=ca NOPBC ignore the periodic boundary conditions when calculating distances

#CV4 contacts between hydrophobic residues calculated as the number of Cbeta carbon couples closer than 0.6 nm 
The GYRATION action with label rgyr calculates the following quantities:
 Quantity   
 Description  
rgyr.value
the radius that was computed from the weightsCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=19,44,171,260,279,295,315,335,372,449,459,478,504,523,540,570,586,602,621 R_0The r_0 parameter of the switching function=0.6 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=hydro

#CV5 the number of salt-bridges calculated as the number of couples of heavy atoms from the charged group closer than 0.6 nm 
#GROUP A is all the heavy atoms from RCOO- group of aspartic acids and glutamic acids 
#GROUP B is all the heavy atoms from RHN3+ from lysines or (RNHC(NH2)2+) of arginines
The COORDINATION action with label hydro calculates the following quantities:
 Quantity   
 Description  
hydro.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=10,11,12,35,36,37,108,109,110,162,163,164,351,352,353,363,364,365 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=75,76,77,78,79,80,81,250,251,252,253,432,433,434,435 R_0The r_0 parameter of the switching function=0.6 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=salt

#CV6 correlation between consecutive psi torsion angles.
The COORDINATION action with label salt calculates the following quantities:
 Quantity   
 Description  
salt.value
the value of the coordinationDIHCORMeasures the degree of similarity between dihedral angles. More details ...
ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS4the set of 8 atoms that are being used each of the dihedral correlation values=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. ,@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS5the set of 8 atoms that are being used each of the dihedral correlation values=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. ,@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS6the set of 8 atoms that are being used each of the dihedral correlation values=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. ,@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS7the set of 8 atoms that are being used each of the dihedral correlation values=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. ,@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS8the set of 8 atoms that are being used each of the dihedral correlation values=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. ,@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS9the set of 8 atoms that are being used each of the dihedral correlation values=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. ,@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS10the set of 8 atoms that are being used each of the dihedral correlation values=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. ,@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS11the set of 8 atoms that are being used each of the dihedral correlation values=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. ,@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS12the set of 8 atoms that are being used each of the dihedral correlation values=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. ,@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS13the set of 8 atoms that are being used each of the dihedral correlation values=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. ,@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS14the set of 8 atoms that are being used each of the dihedral correlation values=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. ,@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS15the set of 8 atoms that are being used each of the dihedral correlation values=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. ,@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS16the set of 8 atoms that are being used each of the dihedral correlation values=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. ,@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS17the set of 8 atoms that are being used each of the dihedral correlation values=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. ,@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS18the set of 8 atoms that are being used each of the dihedral correlation values=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. ,@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
ATOMS19the set of 8 atoms that are being used each of the dihedral correlation values=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. ,@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS20the set of 8 atoms that are being used each of the dihedral correlation values=@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. ,@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS21the set of 8 atoms that are being used each of the dihedral correlation values=@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. ,@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS22the set of 8 atoms that are being used each of the dihedral correlation values=@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. ,@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS23the set of 8 atoms that are being used each of the dihedral correlation values=@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. ,@psi-24the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS24the set of 8 atoms that are being used each of the dihedral correlation values=@psi-24the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. ,@psi-25the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS25the set of 8 atoms that are being used each of the dihedral correlation values=@psi-25the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. ,@psi-26the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS26the set of 8 atoms that are being used each of the dihedral correlation values=@psi-26the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. ,@psi-27the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS27the set of 8 atoms that are being used each of the dihedral correlation values=@psi-27the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. ,@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS28the set of 8 atoms that are being used each of the dihedral correlation values=@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. ,@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS29the set of 8 atoms that are being used each of the dihedral correlation values=@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. ,@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS30the set of 8 atoms that are being used each of the dihedral correlation values=@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. ,@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS31the set of 8 atoms that are being used each of the dihedral correlation values=@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. ,@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS32the set of 8 atoms that are being used each of the dihedral correlation values=@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. ,@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS33the set of 8 atoms that are being used each of the dihedral correlation values=@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. ,@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS34the set of 8 atoms that are being used each of the dihedral correlation values=@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. ,@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS35the set of 8 atoms that are being used each of the dihedral correlation values=@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. ,@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS36the set of 8 atoms that are being used each of the dihedral correlation values=@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. ,@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS37the set of 8 atoms that are being used each of the dihedral correlation values=@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. ,@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS38the set of 8 atoms that are being used each of the dihedral correlation values=@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. ,@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS39the set of 8 atoms that are being used each of the dihedral correlation values=@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. ,@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS40the set of 8 atoms that are being used each of the dihedral correlation values=@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. ,@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
LABELa label for the action so that its output can be referenced in the input to other actions=dihcor
NOPBC ignore the periodic boundary conditions when calculating distances
... DIHCOR

# --- End of included input --- 
#include file with definition of metadynamics CVs involving the small molecule
The DIHCOR action with label dihcor calculates the following quantities:
 Quantity   
 Description  
dihcor.value
the sum of all the dihedral correlationsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=CVs_drug.dat
# The command:
# INCLUDE FILE=CVs_drug.dat
# ensures PLUMED loads the contents of the file called CVs_drug.dat
# The contents of this file are shown below (click the red comment to hide them).
#This is the metadynamics CV file for CVs involving the small molecule

#BELOW ARE SOME CVS BETWEEN 14 regions and the ligand based on CA atoms
The INCLUDE action with label CVs_drug.dat calculates somethingmol: 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)=../system/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=ligan

# AB42 region 1, res 1-3
The GROUP action with label mol calculates somethingCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5,17,27 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg1
 
# AB42 region 2, res 4-6
The COORDINATION action with label reg1 calculates the following quantities:
 Quantity   
 Description  
reg1.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=42,62,86 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg2

# AB42 region 3, res 7-9
The COORDINATION action with label reg2 calculates the following quantities:
 Quantity   
 Description  
reg2.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=103,115,126 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg3

# AB42 region 4, res 10-12
The COORDINATION action with label reg3 calculates the following quantities:
 Quantity   
 Description  
reg3.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=133,154,169 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg4

# AB42 region 5, res 13-15
The COORDINATION action with label reg4 calculates the following quantities:
 Quantity   
 Description  
reg4.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=185,202,219 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg5

# AB42 region 6, res 16-18
The COORDINATION action with label reg5 calculates the following quantities:
 Quantity   
 Description  
reg5.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=236,258,277 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg6

# AB42 region 7, res 19-21
The COORDINATION action with label reg6 calculates the following quantities:
 Quantity   
 Description  
reg6.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=293,313,333 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg7

# AB42 region 8, res 22-24
The COORDINATION action with label reg7 calculates the following quantities:
 Quantity   
 Description  
reg7.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=343,358,370 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg8

# AB42 region 9, res 25-27
The COORDINATION action with label reg8 calculates the following quantities:
 Quantity   
 Description  
reg8.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=386,393,404 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg9

# AB42 region 10, res 28-30
The COORDINATION action with label reg9 calculates the following quantities:
 Quantity   
 Description  
reg9.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=418,440,447 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg10

# AB42 region 11, res 31-33
The COORDINATION action with label reg10 calculates the following quantities:
 Quantity   
 Description  
reg10.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=457,476,495 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg11

# AB42 region 12, res 34-36
The COORDINATION action with label reg11 calculates the following quantities:
 Quantity   
 Description  
reg11.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=502,521,538 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg12

# AB42 region 13, res 37-39
The COORDINATION action with label reg12 calculates the following quantities:
 Quantity   
 Description  
reg12.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=554,561,568 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg13

# AB42 region 14, res 40-42
The COORDINATION action with label reg13 calculates the following quantities:
 Quantity   
 Description  
reg13.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=584,600,619 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=mol R_0The r_0 parameter of the switching function=1.0 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=reg14

# Ligand soft dihedrals
The COORDINATION action with label reg14 calculates the following quantities:
 Quantity   
 Description  
reg14.value
the value of the coordinationligtor1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=641,628,629,640 NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label ligtor1 calculates the following quantities:
 Quantity   
 Description  
ligtor1.value
the TORSION involving these atomsligtor2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=642,641,628,629 NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label ligtor2 calculates the following quantities:
 Quantity   
 Description  
ligtor2.value
the TORSION involving these atomsligtor3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=634,635,636,637 NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label ligtor3 calculates the following quantities:
 Quantity   
 Description  
ligtor3.value
the TORSION involving these atomsligtor4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=641,646,647,648 NOPBC ignore the periodic boundary conditions when calculating distances

# --- End of included input --- 
# Chemical shifts at 278 K
The TORSION action with label ligtor4 calculates the following quantities:
 Quantity   
 Description  
ligtor4.value
the TORSION involving these atomscs: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=1-627 DATADIR The folder with the experimental chemical shifts=../data NOPBC ignore the periodic boundary conditions when calculating distances TEMPLATE A PDB file of the protein system=../system/template.pdb

#activate parallel bias metadynamics
The CS2BACKBONE action with label cs calculates the following quantities:
 Quantity   
 Description  
cs.score
the Metainference score
cs.sigma
uncertainty parameter
cs.sigmaMean
uncertainty in the mean estimate
cs.neff
effective number of replicas
cs.acceptSigma
MC acceptance for sigma values
cs.ha
the calculated Ha hydrogen chemical shifts
cs.hn
the calculated H hydrogen chemical shifts
cs.nh
the calculated N nitrogen chemical shifts
cs.ca
the calculated Ca carbon chemical shifts
cs.cb
the calculated Cb carbon chemical shifts
cs.co
the calculated C' carbon chemical shifts
cs.expha
the experimental Ha hydrogen chemical shifts
cs.exphn
the experimental H hydrogen chemical shifts
cs.expnh
the experimental N nitrogen chemical shifts
cs.expca
the experimental Ca carbon chemical shifts
cs.expcb
the experimental Cb carbon chemical shifts
cs.expco
the experimental C' carbon chemical shifts
cs.value
the backbone chemical shiftsPBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4
    HEIGHTthe height of the Gaussian hills, one for all biases=1.2
    BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=49 #10*SQRT(NUM_OF_CVS)
    SIGMAthe widths of the Gaussian hills=0.64,0.33,0.03,0.69,2.75,1.34,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.1,0.1,0.1,0.1
    PACEthe frequency for hill addition, one for all biases=500
    GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-pi,-pi,-pi,-pi
    GRID_MAXthe upper bounds for the grid=100,100,20,200,400,50,150,150,150,150,150,150,150,150,150,150,150,150,150,150,pi,pi,pi,pi
    GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.1,0.01,0.1,0.1,0.01,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01,0.01,0.01,0.01    
    GRID_WSTRIDEfrequency for dumping the grid=10000
    #GRID_RFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.hydro,GRID.salt,GRID.dihcor,GRID.reg1,GRID.reg2,GRID.reg3,GRID.reg4,GRID.reg5,GRID.reg6,GRID.reg7,GRID.reg8,GRID.reg9,GRID.reg10,GRID.reg11,GRID.reg12,GRID.reg13,GRID.reg14,GRID.ligtor1,GRID.ligtor2,GRID.ligtor3,GRID.ligtor4
    FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcor,HILLS_reg1,HILLS_reg2,HILLS_reg3,HILLS_reg4,HILLS_reg5,HILLS_reg6,HILLS_reg7,HILLS_reg8,HILLS_reg9,HILLS_reg10,HILLS_reg11,HILLS_reg12,HILLS_reg13,HILLS_reg14,HILLS_ligtor1,HILLS_ligtor2,HILLS_ligtor3,HILLS_ligtor4
    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=pbmetad
... PBMETAD

# Metainference - one sigma per nucleus
The PBMETAD action with label pbmetad calculates the following quantities:
 Quantity   
 Description  
pbmetad.bias
the instantaneous value of the bias potentialcs_ha: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.ha-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expha-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_ha
The METAINFERENCE action with label cs_ha calculates the following quantities:
 Quantity   
 Description  
cs_ha.bias
the instantaneous value of the bias potential
cs_ha.sigma
uncertainty parameter
cs_ha.sigmaMean
uncertainty in the mean estimate
cs_ha.neff
effective number of replicas
cs_ha.acceptSigma
MC acceptance for sigma values
cs_ha.weight
weights of the weighted average
cs_ha.biasDer
derivatives with respect to the biascs_hn: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.hn-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.exphn-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_hn
The METAINFERENCE action with label cs_hn calculates the following quantities:
 Quantity   
 Description  
cs_hn.bias
the instantaneous value of the bias potential
cs_hn.sigma
uncertainty parameter
cs_hn.sigmaMean
uncertainty in the mean estimate
cs_hn.neff
effective number of replicas
cs_hn.acceptSigma
MC acceptance for sigma values
cs_hn.weight
weights of the weighted average
cs_hn.biasDer
derivatives with respect to the biascs_nh: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.nh-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expnh-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_nh
The METAINFERENCE action with label cs_nh calculates the following quantities:
 Quantity   
 Description  
cs_nh.bias
the instantaneous value of the bias potential
cs_nh.sigma
uncertainty parameter
cs_nh.sigmaMean
uncertainty in the mean estimate
cs_nh.neff
effective number of replicas
cs_nh.acceptSigma
MC acceptance for sigma values
cs_nh.weight
weights of the weighted average
cs_nh.biasDer
derivatives with respect to the biascs_ca: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.ca-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expca-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_ca
The METAINFERENCE action with label cs_ca calculates the following quantities:
 Quantity   
 Description  
cs_ca.bias
the instantaneous value of the bias potential
cs_ca.sigma
uncertainty parameter
cs_ca.sigmaMean
uncertainty in the mean estimate
cs_ca.neff
effective number of replicas
cs_ca.acceptSigma
MC acceptance for sigma values
cs_ca.weight
weights of the weighted average
cs_ca.biasDer
derivatives with respect to the biascs_cb: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.cb-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expcb-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_cb
The METAINFERENCE action with label cs_cb calculates the following quantities:
 Quantity   
 Description  
cs_cb.bias
the instantaneous value of the bias potential
cs_cb.sigma
uncertainty parameter
cs_cb.sigmaMean
uncertainty in the mean estimate
cs_cb.neff
effective number of replicas
cs_cb.acceptSigma
MC acceptance for sigma values
cs_cb.weight
weights of the weighted average
cs_cb.biasDer
derivatives with respect to the biascs_co: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.co-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expco-.*) SIGMA0 initial value of the uncertainty parameter=9.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_co

# Ensemble statistics
The METAINFERENCE action with label cs_co calculates the following quantities:
 Quantity   
 Description  
cs_co.bias
the instantaneous value of the bias potential
cs_co.sigma
uncertainty parameter
cs_co.sigmaMean
uncertainty in the mean estimate
cs_co.neff
effective number of replicas
cs_co.acceptSigma
MC acceptance for sigma values
cs_co.weight
weights of the weighted average
cs_co.biasDer
derivatives with respect to the biasens: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(cs\.ha-.*),(cs\.hn-.*),(cs\.nh-.*),(cs\.ca-.*),(cs\.cb-.*),(cs\.co-.*),pbmetad.bias REWEIGHT simple REWEIGHT using the latest ARG as energy

The ENSEMBLE action with label ens calculates the following quantities:
 Quantity   
 Description  
ens..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsSTATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ...
    ARGthe labels of the values from which the function is calculated=(ens\.cs\.ha-.*),(ens\.cs\.hn-.*),(ens\.cs\.nh-.*),(ens\.cs\.ca-.*),(ens\.cs\.cb-.*),(ens\.cs\.co-.*)
    PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(cs\.expha-.*),(cs\.exphn-.*),(cs\.expnh-.*),(cs\.expca-.*),(cs\.expcb-.*),(cs\.expco-.*) 
    LABELa label for the action so that its output can be referenced in the input to other actions=stat
... STATS

The STATS action with label stat calculates the following quantities:
 Quantity   
 Description  
stat.sqdevsum
the sum of the squared deviations between arguments and parameters
stat.corr
the correlation between arguments and parameters
stat.slope
the slope of a linear fit between arguments and parameters
stat.intercept
the intercept of a linear fit between arguments and parametersPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4,pbmetad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(ens.*),(stat.*) FILEthe name of the file on which to output these quantities=STATS STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_ha.*) FILEthe name of the file on which to output these quantities=BAYES.HA STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_hn.*) FILEthe name of the file on which to output these quantities=BAYES.HN STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_nh.*) FILEthe name of the file on which to output these quantities=BAYES.NH STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_ca.*) FILEthe name of the file on which to output these quantities=BAYES.CA STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_cb.*) FILEthe name of the file on which to output these quantities=BAYES.CB STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_co.*) FILEthe name of the file on which to output these quantities=BAYES.CO STRIDE the frequency with which the quantities of interest should be output=500
ENDPLUMEDTerminate plumed input. More details