PLUMED-NEST

Project ID: plumID:25.018
Source: ./dsRBD_dimer/plumed.dat
Originally used with PLUMED version: 2.9
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
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=./dimer_cg.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=1-265 ENTITY1the atoms that make up a molecule that you wish to align=266-530

#Centroid for Backbone beads of the structured regions in the traditional dsRBD
com_a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=10,14,17,19,21,23,25,27,29,30,32,45,48,52,54,56,60,77,79,83,85,86,88,90,86,98,100,117,120,123,125,126,128,131,133,134,135,137,138,139,144,146,148,150,153,155,157,158,161,163
The CENTER action with label com_a calculates the following quantities:
 Quantity   
 Description  
com_a.value
the position of the center of masscom_b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=275,279,282,284,286,288,290,292,294,295,297,310,313,317,319,321,325,342,344,348,350,351,353,355,361,363,365,382,385,388,390,391,393,396,398,399,400,402,403,404,409,411,413,415,418,420,422,423,426,428

#Centroids of BB beads for secondary stucutres for unit A
The CENTER action with label com_b calculates the following quantities:
 Quantity   
 Description  
com_b.value
the position of the center of massheli_1a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=10,14,17,19,21,23,25,27,29,30,32
The CENTER action with label heli_1a calculates the following quantities:
 Quantity   
 Description  
heli_1a.value
the position of the center of massbeta_1a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=45,48,52,54,56,60
The CENTER action with label beta_1a calculates the following quantities:
 Quantity   
 Description  
beta_1a.value
the position of the center of massbeta_2a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=77,79,83,85,86,88,90
The CENTER action with label beta_2a calculates the following quantities:
 Quantity   
 Description  
beta_2a.value
the position of the center of massbeta_3a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=86,98,100
The CENTER action with label beta_3a calculates the following quantities:
 Quantity   
 Description  
beta_3a.value
the position of the center of massheli_2a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=117,120,123,125,126,128,131,133,134,135,137,138,139,144,146,148,150,153,155,157,158,161,163
The CENTER action with label heli_2a calculates the following quantities:
 Quantity   
 Description  
heli_2a.value
the position of the center of massheli_3a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=187,189,191,193,195,197,199,201,202,205,206,208,210,212

#Centroids of BB beads for secondary stucutres for unit B
The CENTER action with label heli_3a calculates the following quantities:
 Quantity   
 Description  
heli_3a.value
the position of the center of massheli_1b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=275,279,282,284,286,288,290,292,294,295,297
The CENTER action with label heli_1b calculates the following quantities:
 Quantity   
 Description  
heli_1b.value
the position of the center of massbeta_1b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=310,313,317,319,321,325
The CENTER action with label beta_1b calculates the following quantities:
 Quantity   
 Description  
beta_1b.value
the position of the center of massbeta_2b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=342,344,348,350,351,353,355
The CENTER action with label beta_2b calculates the following quantities:
 Quantity   
 Description  
beta_2b.value
the position of the center of massbeta_3b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=361,363,365
The CENTER action with label beta_3b calculates the following quantities:
 Quantity   
 Description  
beta_3b.value
the position of the center of massheli_2b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=382,385,388,390,391,393,396,398,399,400,402,403,404,409,411,413,415,418,420,422,423,426,428
The CENTER action with label heli_2b calculates the following quantities:
 Quantity   
 Description  
heli_2b.value
the position of the center of massheli_3b: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=452,454,456,458,460,462,464,466,467,470,471,473,475,477

The CENTER action with label heli_3b calculates the following quantities:
 Quantity   
 Description  
heli_3b.value
the position of the center of masscom_distance: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com_a,com_b #Distance between the centroids of the traditional dsRBDs
The DISTANCE action with label com_distance calculates the following quantities:
 Quantity   
 Description  
com_distance.value
the DISTANCE between this pair of atomssub_ori: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=heli_3a,beta_2a,beta_2b,heli_3b # Torsion angle defining orientation 

The TORSION action with label sub_ori calculates the following quantities:
 Quantity   
 Description  
sub_ori.value
the TORSION involving these atomsrg: 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=10,14,17,19,21,23,25,27,29,30,32,45,48,52,54,56,60,77,79,83,85,86,88,90,86,98,100,117,120,123,125,126,128,131,133,134,135,137,138,139,144,146,148,150,153,155,157,158,161,163,187,189,191,193,195,197,199,201,202,205,206,208,210,212,275,279,282,284,286,288,290,292,294,295,297,310,313,317,319,321,325,342,344,348,350,351,353,355,361,363,365,382,385,388,390,391,393,396,398,399,400,402,403,404,409,411,413,415,418,420,422,423,426,428,452,454,456,458,460,462,464,466,467,470,471,473,475,477

The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsrg_wall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg ATthe positions of the wall=3.1 KAPPAthe force constant for the wall=500

#Distance from Helix-1 of unit A

The UPPER_WALLS action with label rg_wall calculates the following quantities:
 Quantity   
 Description  
rg_wall.bias
the instantaneous value of the bias potential
rg_wall.force2
the instantaneous value of the squared force due to this bias potentialh1a_h1b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,heli_1b
The DISTANCE action with label h1a_h1b calculates the following quantities:
 Quantity   
 Description  
h1a_h1b.value
the DISTANCE between this pair of atomsh1a_b1b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,beta_1b
The DISTANCE action with label h1a_b1b calculates the following quantities:
 Quantity   
 Description  
h1a_b1b.value
the DISTANCE between this pair of atomsh1a_b2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,beta_2b
The DISTANCE action with label h1a_b2b calculates the following quantities:
 Quantity   
 Description  
h1a_b2b.value
the DISTANCE between this pair of atomsh1a_b3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,beta_3b
The DISTANCE action with label h1a_b3b calculates the following quantities:
 Quantity   
 Description  
h1a_b3b.value
the DISTANCE between this pair of atomsh1a_h2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,heli_2b
The DISTANCE action with label h1a_h2b calculates the following quantities:
 Quantity   
 Description  
h1a_h2b.value
the DISTANCE between this pair of atomsh1a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1a,heli_3b

# Distance from Beta-1 of unit A

The DISTANCE action with label h1a_h3b calculates the following quantities:
 Quantity   
 Description  
h1a_h3b.value
the DISTANCE between this pair of atomsb1a_b1b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1a,beta_1b
The DISTANCE action with label b1a_b1b calculates the following quantities:
 Quantity   
 Description  
b1a_b1b.value
the DISTANCE between this pair of atomsb1a_b2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1a,beta_2b
The DISTANCE action with label b1a_b2b calculates the following quantities:
 Quantity   
 Description  
b1a_b2b.value
the DISTANCE between this pair of atomsb1a_b3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1a,beta_3b
The DISTANCE action with label b1a_b3b calculates the following quantities:
 Quantity   
 Description  
b1a_b3b.value
the DISTANCE between this pair of atomsb1a_h2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1a,heli_2b
The DISTANCE action with label b1a_h2b calculates the following quantities:
 Quantity   
 Description  
b1a_h2b.value
the DISTANCE between this pair of atomsb1a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1a,heli_3b

#Distance from Beta-2 of unit A

The DISTANCE action with label b1a_h3b calculates the following quantities:
 Quantity   
 Description  
b1a_h3b.value
the DISTANCE between this pair of atomsb2a_b2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2a,beta_2b
The DISTANCE action with label b2a_b2b calculates the following quantities:
 Quantity   
 Description  
b2a_b2b.value
the DISTANCE between this pair of atomsb2a_b3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2a,beta_3b
The DISTANCE action with label b2a_b3b calculates the following quantities:
 Quantity   
 Description  
b2a_b3b.value
the DISTANCE between this pair of atomsb2a_h2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2a,heli_2b
The DISTANCE action with label b2a_h2b calculates the following quantities:
 Quantity   
 Description  
b2a_h2b.value
the DISTANCE between this pair of atomsb2a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2a,heli_3b

#Distance from Beta-3 of unit A

The DISTANCE action with label b2a_h3b calculates the following quantities:
 Quantity   
 Description  
b2a_h3b.value
the DISTANCE between this pair of atomsb3a_b3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_3a,beta_3b
The DISTANCE action with label b3a_b3b calculates the following quantities:
 Quantity   
 Description  
b3a_b3b.value
the DISTANCE between this pair of atomsb3a_h2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_3a,heli_2b
The DISTANCE action with label b3a_h2b calculates the following quantities:
 Quantity   
 Description  
b3a_h2b.value
the DISTANCE between this pair of atomsb3a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_3a,heli_3b

#Distance from Helix-2 of unit A

The DISTANCE action with label b3a_h3b calculates the following quantities:
 Quantity   
 Description  
b3a_h3b.value
the DISTANCE between this pair of atomsh2a_h2b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_2a,heli_2b
The DISTANCE action with label h2a_h2b calculates the following quantities:
 Quantity   
 Description  
h2a_h2b.value
the DISTANCE between this pair of atomsh2a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_2a,heli_3b

#Distance from Helix-3 of unit A

The DISTANCE action with label h2a_h3b calculates the following quantities:
 Quantity   
 Description  
h2a_h3b.value
the DISTANCE between this pair of atomsh3a_h3b: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_3a,heli_3b

#Distance from Helix-1 of unit B

The DISTANCE action with label h3a_h3b calculates the following quantities:
 Quantity   
 Description  
h3a_h3b.value
the DISTANCE between this pair of atomsh1b_b1a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1b,beta_1a
The DISTANCE action with label h1b_b1a calculates the following quantities:
 Quantity   
 Description  
h1b_b1a.value
the DISTANCE between this pair of atomsh1b_b2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1b,beta_2a
The DISTANCE action with label h1b_b2a calculates the following quantities:
 Quantity   
 Description  
h1b_b2a.value
the DISTANCE between this pair of atomsh1b_b3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1b,beta_3a
The DISTANCE action with label h1b_b3a calculates the following quantities:
 Quantity   
 Description  
h1b_b3a.value
the DISTANCE between this pair of atomsh1b_h2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1b,heli_2a
The DISTANCE action with label h1b_h2a calculates the following quantities:
 Quantity   
 Description  
h1b_h2a.value
the DISTANCE between this pair of atomsh1b_h3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_1b,heli_3a

# Distance from Beta-1 of unit B

The DISTANCE action with label h1b_h3a calculates the following quantities:
 Quantity   
 Description  
h1b_h3a.value
the DISTANCE between this pair of atomsb1b_b2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1b,beta_2a
The DISTANCE action with label b1b_b2a calculates the following quantities:
 Quantity   
 Description  
b1b_b2a.value
the DISTANCE between this pair of atomsb1b_b3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1b,beta_3a
The DISTANCE action with label b1b_b3a calculates the following quantities:
 Quantity   
 Description  
b1b_b3a.value
the DISTANCE between this pair of atomsb1b_h2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1b,heli_2a
The DISTANCE action with label b1b_h2a calculates the following quantities:
 Quantity   
 Description  
b1b_h2a.value
the DISTANCE between this pair of atomsb1b_h3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_1b,heli_3a

#Distance from Beta-2 of unit B

The DISTANCE action with label b1b_h3a calculates the following quantities:
 Quantity   
 Description  
b1b_h3a.value
the DISTANCE between this pair of atomsb2b_b3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2b,beta_3a
The DISTANCE action with label b2b_b3a calculates the following quantities:
 Quantity   
 Description  
b2b_b3a.value
the DISTANCE between this pair of atomsb2b_h2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2b,heli_2a
The DISTANCE action with label b2b_h2a calculates the following quantities:
 Quantity   
 Description  
b2b_h2a.value
the DISTANCE between this pair of atomsb2b_h3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_2b,heli_3a

#Distance from Beta-3 of unit B

The DISTANCE action with label b2b_h3a calculates the following quantities:
 Quantity   
 Description  
b2b_h3a.value
the DISTANCE between this pair of atomsb3b_h2a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_3b,heli_2a
The DISTANCE action with label b3b_h2a calculates the following quantities:
 Quantity   
 Description  
b3b_h2a.value
the DISTANCE between this pair of atomsb3b_h3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta_3b,heli_3a

#Distance from Helix-2 of unit B

The DISTANCE action with label b3b_h3a calculates the following quantities:
 Quantity   
 Description  
b3b_h3a.value
the DISTANCE between this pair of atomsh2b_h3a: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=heli_2b,heli_3a


The DISTANCE action with label h2b_h3a calculates the following quantities:
 Quantity   
 Description  
h2b_h3a.value
the DISTANCE between this pair of atomsSAXSCalculates SAXS intensity. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxsdata
ATOMSThe atoms to be included in the calculation, e=1-530
NOPBC Ignore the periodic boundary conditions when calculating distances

MARTINI Calculate SAXS for a Martini model

#SCALE_EXPINT=2.369868e-01

QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.051980e-02    EXPINT1Add an experimental value for each q value=1.685175e-01
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =4.037760e-02    EXPINT2Add an experimental value for each q value=1.437632e-01
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =5.023550e-02    EXPINT3Add an experimental value for each q value=1.158607e-01
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =6.009330e-02    EXPINT4Add an experimental value for each q value=9.361882e-02
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =7.077260e-02    EXPINT5Add an experimental value for each q value=7.528224e-02
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =8.063050e-02    EXPINT6Add an experimental value for each q value=5.869592e-02
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =9.048830e-02    EXPINT7Add an experimental value for each q value=4.661092e-02
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.003460e-01    EXPINT8Add an experimental value for each q value=3.780474e-02
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.102040e-01    EXPINT9Add an experimental value for each q value=2.888539e-02
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.200620e-01   EXPINT10Add an experimental value for each q value=2.381342e-02
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.307410e-01   EXPINT11Add an experimental value for each q value=1.854355e-02
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.405990e-01   EXPINT12Add an experimental value for each q value=1.513408e-02
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.504570e-01   EXPINT13Add an experimental value for each q value=1.168382e-02
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.603150e-01   EXPINT14Add an experimental value for each q value=9.586579e-03
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.701730e-01   EXPINT15Add an experimental value for each q value=7.846184e-03
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.800300e-01   EXPINT16Add an experimental value for each q value=6.377632e-03
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.907100e-01   EXPINT17Add an experimental value for each q value=5.481711e-03
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.005680e-01   EXPINT18Add an experimental value for each q value=4.510658e-03
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.104250e-01   EXPINT19Add an experimental value for each q value=1.936316e-03
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.202830e-01   EXPINT20Add an experimental value for each q value=2.900658e-03
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.301410e-01   EXPINT21Add an experimental value for each q value=2.972895e-03
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.408200e-01   EXPINT22Add an experimental value for each q value=3.027368e-03
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.506780e-01   EXPINT23Add an experimental value for each q value=2.162763e-03
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.605360e-01   EXPINT24Add an experimental value for each q value=2.088553e-03
QVALUE25Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.703940e-01   EXPINT25Add an experimental value for each q value=2.220789e-03
QVALUE26Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.802520e-01   EXPINT26Add an experimental value for each q value=2.259079e-03
QVALUE27Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =2.901100e-01   EXPINT27Add an experimental value for each q value=1.329474e-03
QVALUE28Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.007890e-01   EXPINT28Add an experimental value for each q value=1.840263e-03
QVALUE29Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.106470e-01   EXPINT29Add an experimental value for each q value=1.931447e-03
QVALUE30Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.205050e-01   EXPINT30Add an experimental value for each q value=1.415000e-03
QVALUE31Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.303620e-01   EXPINT31Add an experimental value for each q value=1.307763e-03
QVALUE32Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.402200e-01   EXPINT32Add an experimental value for each q value=8.793421e-04
QVALUE33Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =3.500780e-01   EXPINT33Add an experimental value for each q value=1.732237e-03
...

The SAXS action with label saxsdata calculates the following quantities:
 Quantity   
 Description  
saxsdata.score
the Metainference score
saxsdata.sigma
uncertainty parameter
saxsdata.sigmaMean
uncertainty in the mean estimate
saxsdata.neff
effective number of replicas
saxsdata.acceptSigma
MC acceptance for sigma values
saxsdata.q
The # SAXS of qlsaxs: STATSCalculates 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=(saxsdata\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsdata\.exp-.*)

The STATS action with label lsaxs calculates the following quantities:
 Quantity   
 Description  
lsaxs.sqdevsum
the sum of the squared deviations between arguments and parameters
lsaxs.corr
the correlation between arguments and parameters
lsaxs.slope
the slope of a linear fit between arguments and parameters
lsaxs.intercept
the intercept of a linear fit between arguments and parametersPBMETADUsed to performed Parallel Bias metadynamics. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=pbmetad
ARGthe labels of the scalars on which the bias will act=com_distance,sub_ori,rg
HEIGHTthe height of the Gaussian hills, one for all biases=0.1
PACEthe frequency for hill addition, one for all biases=100
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=20
#ADAPTIVE=DIFF
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID.com_distance,GRID.sub_ori,GRID.rg
GRID_WSTRIDEfrequency for dumping the grid=2000
#GRID_RFILES=GRID.com_distance,GRID.sub_ori,GRID.rg
SIGMAthe widths of the Gaussian hills=0.4,0.6,0.1
#SIGMA_MIN=0.005,0.005,0.005
#SIGMA_MAX=0.2,0.2,0.2

GRID_MINthe lower bounds for the grid=1.0,-pi,1.0
GRID_MAXthe upper bounds for the grid=20,pi,10

WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
#UPDATE_FROM=2000
... PBMETAD

The PBMETAD action with label pbmetad calculates the following quantities:
 Quantity   
 Description  
pbmetad.bias
the instantaneous value of the bias potentialMETAINFERENCECalculates the Metainference energy for a set of experimental data. More details ...
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas
AVERAGINGStride for calculation of averaged weights and sigma_mean=100
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MOUTLIERS
ARGthe labels of the scalars on which the bias will act=(saxsdata\.q-.*),pbmetad.bias REWEIGHT simple REWEIGHT using the latest ARG as energy PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(saxsdata\.exp-.*)
SCALE_PRIOR either FLAT or GAUSSIAN=GAUSSIAN
ADDOFFSET Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_PRIOR either FLAT or GAUSSIAN=GAUSSIAN
OFFSET0 initial value of the offset=0 DOFFSETmaximum MC move of the offset=0.002
SCALE0 initial value of the scaling factor=0.20 DSCALEmaximum MC move of the scaling factor=0.00005
SIGMA0 initial value of the uncertainty parameter=0.001 SIGMA_MIN minimum value of the uncertainty parameter=0. SIGMA_MAX maximum value of the uncertainty parameter=1 DSIGMAmaximum MC move of the uncertainty parameter=0.0001
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM
LABELa label for the action so that its output can be referenced in the input to other actions=metainf
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
STRIDEthe frequency with which the forces due to the bias should be calculated=2
... METAINFERENCE

The METAINFERENCE action with label metainf calculates the following quantities:
 Quantity   
 Description  
metainf.bias
the instantaneous value of the bias potential
metainf.sigma
uncertainty parameter
metainf.sigmaMean
uncertainty in the mean estimate
metainf.neff
effective number of replicas
metainf.acceptSigma
MC acceptance for sigma values
metainf.acceptScale
MC acceptance for scale value
metainf.weight
weights of the weighted average
metainf.biasDer
derivatives with respect to the bias
metainf.scale
scale parameter
metainf.offset
offset parameterensaxs: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(saxsdata\.q-.*),pbmetad.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label ensaxs calculates the following quantities:
 Quantity   
 Description  
ensaxs..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsstatsq: STATSCalculates 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=(ensaxs\.saxsdata\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsdata\.exp-.*)

The STATS action with label statsq calculates the following quantities:
 Quantity   
 Description  
statsq.sqdevsum
the sum of the squared deviations between arguments and parameters
statsq.corr
the correlation between arguments and parameters
statsq.slope
the slope of a linear fit between arguments and parameters
statsq.intercept
the intercept of a linear fit between arguments and parametersFLUSHThis 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.q-.*),(saxsdata\.exp-.*) FILEthe name of the file on which to output these quantities=CV.dat STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=RESTRAINTS ARGthe labels of the values that you would like to print to the file=metainf.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=q.dat ARGthe labels of the values that you would like to print to the file=statsq.*,lsaxs.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=Analyse.dat ARGthe labels of the values that you would like to print to the file=com_distance,sub_ori,rg STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=BIAS ARGthe labels of the values that you would like to print to the file=pbmetad.bias STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENSAXS ARGthe labels of the values that you would like to print to the file=(ensaxs\.saxsdata\.q-.*) STRIDE the frequency with which the quantities of interest should be output=100

enANA: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=com_distance,sub_ori,rg,pbmetad.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label enANA calculates the following quantities:
 Quantity   
 Description  
enANA..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsPRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENANA ARGthe labels of the values that you would like to print to the file=enANA.* STRIDE the frequency with which the quantities of interest should be output=100

PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=PARS_ALL ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=100