PLUMED-NEST-TEST-SITE

Project ID: plumID:22.023
Source: PRODUCTION/plumed.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

# 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

# Tail definitions
The TORSION action with label disulf8 calculates the following quantities:
 Quantity   
 Description  
disulf8.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

# Inter-tail contacts
# Theoretical maximum: 3828
The GROUP action with label tail15 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

# 1
The COORDINATION action with label con7 calculates the following quantities:
 Quantity   
 Description  
con7.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

The TORSION action with label tor8 calculates the following quantities:
 Quantity   
 Description  
tor8.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=200 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR LABELa label for the action so that its output can be referenced in the input to other actions=pb GRID_WSTRIDEfrequency for dumping the grid=10000 SIGMAthe widths of the Gaussian hills=1000 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
    ARGthe labels of the scalars on which the bias will act=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=../HILLS_disulf1,../HILLS_disulf2,../HILLS_disulf3,../HILLS_disulf4,../HILLS_disulf5,../HILLS_disulf6,../HILLS_disulf7,../HILLS_disulf8,../HILLS_tor1,../HILLS_tor2,../HILLS_tor3,../HILLS_tor4,../HILLS_tor5,../HILLS_tor6,../HILLS_tor7,../HILLS_tor8,../HILLS_con1,../HILLS_con2,../HILLS_con3,../HILLS_con4,../HILLS_con5,../HILLS_con6,../HILLS_con7
    GRID_RFILESread grid for the bias=../GRID_disulf1,../GRID_disulf2,../GRID_disulf3,../GRID_disulf4,../GRID_disulf5,../GRID_disulf6,../GRID_disulf7,../GRID_disulf8,../GRID_tor1,../GRID_tor2,../GRID_tor3,../GRID_tor4,../GRID_tor5,../GRID_tor6,../GRID_tor7,../GRID_tor8,../GRID_con1,../GRID_con2,../GRID_con3,../GRID_con4,../GRID_con5,../GRID_con6,../GRID_con7
    GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=../GRID_disulf1,../GRID_disulf2,../GRID_disulf3,../GRID_disulf4,../GRID_disulf5,../GRID_disulf6,../GRID_disulf7,../GRID_disulf8,../GRID_tor1,../GRID_tor2,../GRID_tor3,../GRID_tor4,../GRID_tor5,../GRID_tor6,../GRID_tor7,../GRID_tor8,../GRID_con1,../GRID_con2,../GRID_con3,../GRID_con4,../GRID_con5,../GRID_con6,../GRID_con7
...

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

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

# print useful info to file
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=gmm.* FILEthe name of the file on which to output these quantities=EMMI 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=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 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