PLUMED-NEST

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

RESTART
Activate restart. More details
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=../structure.pdb

# define all heavy atoms using GROMACS index file
protein-h: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
protein: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein
system: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the 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)
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-537 
ENTITY1
the atoms that make up a molecule that you wish to align
=538-1074 
ENTITY2
the atoms that make up a molecule that you wish to align
=1075-1611 
ENTITY3
the atoms that make up a molecule that you wish to align
=1612-2148 
ENTITY4
the atoms that make up a molecule that you wish to align
=2149-2685 
ENTITY5
the atoms that make up a molecule that you wish to align
=2686-3222 
ENTITY6
the atoms that make up a molecule that you wish to align
=3223-3759 
ENTITY7
the atoms that make up a molecule that you wish to align
=3760-4296 
ENTITY8
the atoms that make up a molecule that you wish to align
=4297-4833 
ENTITY9
the atoms that make up a molecule that you wish to align
=4834-5370 
ENTITY10
the atoms that make up a molecule that you wish to align
=5371-5907 
ENTITY11
the atoms that make up a molecule that you wish to align
=5908-6444 
ENTITY12
the atoms that make up a molecule that you wish to align
=6445-6981 
ENTITY13
the atoms that make up a molecule that you wish to align
=6982-7518 
ENTITY14
the atoms that make up a molecule that you wish to align
=7519-8055 
ENTITY15
the 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
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a 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 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rmsd
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rmsd 
AT
the positions of the wall
=0.3 
KAPPA
the force constant for the wall
=0.0 
EXP
 the powers for the walls
=3 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a 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)
disulf1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=29,32,94,91
The TORSION action with label disulf1 calculates a scalar quantitydisulf2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1103,1106,1168,1165
The TORSION action with label disulf2 calculates a scalar quantitydisulf3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=2177,2180,2242,2239
The TORSION action with label disulf3 calculates a scalar quantitydisulf4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=3251,3254,3316,3313
The TORSION action with label disulf4 calculates a scalar quantitydisulf5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=4325,4328,4390,4387
The TORSION action with label disulf5 calculates a scalar quantitydisulf6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5399,5402,5464,5461
The TORSION action with label disulf6 calculates a scalar quantitydisulf7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=6473,6476,6538,6535
The TORSION action with label disulf7 calculates a scalar quantitydisulf8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7547,7550,7612,7609

# Tail definitions
The TORSION action with label disulf8 calculates a scalar quantitytail1: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail1
tail3: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail3
tail5: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail5
tail7: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail7
tail9: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail9
tail11: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail11
tail13: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail13
tail15: 
GROUP
Define 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_FILE
the name of index file (gromacs syntax)
=../index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=tail15

# Inter-tail contacts
# Theoretical maximum: 3828
con1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail3 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con1 calculates a scalar quantitycon2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail5 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con2 calculates a scalar quantitycon3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail7 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con3 calculates a scalar quantitycon4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail9 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con4 calculates a scalar quantitycon5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail9 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail11 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con5 calculates a scalar quantitycon6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail11 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail13 
R_0
The r_0 parameter of the switching function
=0.8
The COORDINATION action with label con6 calculates a scalar quantitycon7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=tail13 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=tail15 
R_0
The r_0 parameter of the switching function
=0.8

# 1
The COORDINATION action with label con7 calculates a scalar quantitycom-cys2-1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-2
the protein/dna/rna backbone atoms in residue 2. Click here for more information. 
com-cys7-1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-7
the protein/dna/rna backbone atoms in residue 7. Click here for more information. 
com-as14-1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-14
the protein/dna/rna backbone atoms in residue 14. Click here for more information. 
com-as31-1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-31
the protein/dna/rna backbone atoms in residue 31. Click here for more information. 
# 2
com-cys2-2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-76
the protein/dna/rna backbone atoms in residue 76. Click here for more information. 
com-cys7-2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-81
the protein/dna/rna backbone atoms in residue 81. Click here for more information. 
com-as14-2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-88
the protein/dna/rna backbone atoms in residue 88. Click here for more information. 
com-as31-2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-105
the protein/dna/rna backbone atoms in residue 105. Click here for more information. 
# 3
com-cys2-3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-150
the protein/dna/rna backbone atoms in residue 150. Click here for more information. 
com-cys7-3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-155
the protein/dna/rna backbone atoms in residue 155. Click here for more information. 
com-as14-3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-162
the protein/dna/rna backbone atoms in residue 162. Click here for more information. 
com-as31-3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-179
the protein/dna/rna backbone atoms in residue 179. Click here for more information. 
# 4
com-cys2-4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-224
the protein/dna/rna backbone atoms in residue 224. Click here for more information. 
com-cys7-4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-229
the protein/dna/rna backbone atoms in residue 229. Click here for more information. 
com-as14-4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-236
the protein/dna/rna backbone atoms in residue 236. Click here for more information. 
com-as31-4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-253
the protein/dna/rna backbone atoms in residue 253. Click here for more information. 
# 5
com-cys2-5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-298
the protein/dna/rna backbone atoms in residue 298. Click here for more information. 
com-cys7-5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-303
the protein/dna/rna backbone atoms in residue 303. Click here for more information. 
com-as14-5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-310
the protein/dna/rna backbone atoms in residue 310. Click here for more information. 
com-as31-5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-327
the protein/dna/rna backbone atoms in residue 327. Click here for more information. 
# 6
com-cys2-6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-372
the protein/dna/rna backbone atoms in residue 372. Click here for more information. 
com-cys7-6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-377
the protein/dna/rna backbone atoms in residue 377. Click here for more information. 
com-as14-6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-384
the protein/dna/rna backbone atoms in residue 384. Click here for more information. 
com-as31-6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-401
the protein/dna/rna backbone atoms in residue 401. Click here for more information. 
# 7
com-cys2-7: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-446
the protein/dna/rna backbone atoms in residue 446. Click here for more information. 
com-cys7-7: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-451
the protein/dna/rna backbone atoms in residue 451. Click here for more information. 
com-as14-7: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-458
the protein/dna/rna backbone atoms in residue 458. Click here for more information. 
com-as31-7: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-475
the protein/dna/rna backbone atoms in residue 475. Click here for more information. 
# 8
com-cys2-8: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-520
the protein/dna/rna backbone atoms in residue 520. Click here for more information. 
com-cys7-8: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-525
the protein/dna/rna backbone atoms in residue 525. Click here for more information. 
com-as14-8: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-532
the protein/dna/rna backbone atoms in residue 532. Click here for more information. 
com-as31-8: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=
@back-549
the protein/dna/rna backbone atoms in residue 549. Click here for more information. 

# Tail torsion (CYS2:CA,CYS7:CA,ASN14:CA,ASN31:CA)
tor1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitytor8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantity
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
    # Carlo's Biasfactor rule-of-thumb: 10 * sqrt(number of CVs)
    
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=56 
HEIGHT
the height of the Gaussian hills, one for all biases
=0.3 
PACE
the 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
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb 
GRID_WSTRIDE
frequency for dumping the grid
=10000 
SIGMA
the widths of the Gaussian hills
=1000 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
    
ARG
the input for this action is the scalar output from one or more other actions
=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7
    
SIGMA_MIN
the 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_MAX
the 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_MIN
the 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_MAX
the 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
    
FILE
files 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_RFILES
read 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_WFILES
dump 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 potential
EMMI
Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=pb.bias 
REWEIGHT
 simple REWEIGHT using the ARG as energy
    
LABEL
a 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
 
TEMP
temperature
=310.0 
NL_STRIDE
The frequency with which we are updating the neighbor list
=100 
NL_CUTOFF
The cutoff in overlap for the neighbor list
=0.01
    
ATOMS
atoms for which we calculate the density map, typically all heavy atoms
=protein-h 
GMM_FILE
file with the parameters of the GMM components
=../iapp.dat
    # the larger the number the softer the contribution of the EM data
    
SIGMA0
initial value of the uncertainty
=5.0 
SIGMA_MIN
minimum uncertainty
=0.05 
DSIGMA
MC step for uncertainties
=0.1 
RESOLUTION
Cryo-EM map resolution
=0.1 
NOISETYPE
functional form of the noise (GAUSS, OUTLIERS, MARGINAL)
=GAUSS
    OPTSIGMAMEAN SIGMA_MEAN0=2.0
    
AVERAGING
Averaging window for weights
=200 
WRITE_STRIDE
write 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: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=gmm.scoreb 
STRIDE
the 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 file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=gmm 
FILE
the name of the file on which to output these quantities
=EMMI 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500