Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part2_MM/plumed_PB4_MM.dat
Originally used with PLUMED version: 2.7
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
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=../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=1-166
s1The CENTER_FAST action with label s1 calculates the following quantities:| Quantity | Type | Description |
| s1 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-1the protein/dna/rna backbone atoms in residue 1. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s2The CENTER_FAST action with label s2 calculates the following quantities:| Quantity | Type | Description |
| s2 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-2the protein/dna/rna backbone atoms in residue 2. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s3The CENTER_FAST action with label s3 calculates the following quantities:| Quantity | Type | Description |
| s3 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-3the protein/dna/rna backbone atoms in residue 3. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s4The CENTER_FAST action with label s4 calculates the following quantities:| Quantity | Type | Description |
| s4 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-4the protein/dna/rna backbone atoms in residue 4. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s5The CENTER_FAST action with label s5 calculates the following quantities:| Quantity | Type | Description |
| s5 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-5the protein/dna/rna backbone atoms in residue 5. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s6The CENTER_FAST action with label s6 calculates the following quantities:| Quantity | Type | Description |
| s6 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-6the protein/dna/rna backbone atoms in residue 6. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s7The CENTER_FAST action with label s7 calculates the following quantities:| Quantity | Type | Description |
| s7 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-7the protein/dna/rna backbone atoms in residue 7. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s8The CENTER_FAST action with label s8 calculates the following quantities:| Quantity | Type | Description |
| s8 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-8the protein/dna/rna backbone atoms in residue 8. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s9The CENTER_FAST action with label s9 calculates the following quantities:| Quantity | Type | Description |
| s9 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-9the protein/dna/rna backbone atoms in residue 9. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
s10The CENTER_FAST action with label s10 calculates the following quantities:| Quantity | Type | Description |
| s10 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@back-10the protein/dna/rna backbone atoms in residue 10. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
LABELa label for the action so that its output can be referenced in the input to other actions=backThe ALPHABETA action with label back calculates the following quantities:| Quantity | Type | Description |
| back | scalar | the alpha beta CV |
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. COEFFICIENT1the coefficient for each of the torsional angles=-0.01427455
ATOMS2the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. COEFFICIENT2the coefficient for each of the torsional angles=-0.03003557
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. COEFFICIENT3the coefficient for each of the torsional angles=-0.23777775
ATOMS4the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. COEFFICIENT4the coefficient for each of the torsional angles=0.139227
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. COEFFICIENT5the coefficient for each of the torsional angles=0.26525215
ATOMS6the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. COEFFICIENT6the coefficient for each of the torsional angles=-0.18108167
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. COEFFICIENT7the coefficient for each of the torsional angles=0.01530576
ATOMS8the atoms involved for each of the torsions you wish to calculate=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. COEFFICIENT8the coefficient for each of the torsional angles=0.07231603
ATOMS9the atoms involved for each of the torsions you wish to calculate=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. COEFFICIENT9the coefficient for each of the torsional angles=-0.1183752
ATOMS10the atoms involved for each of the torsions you wish to calculate=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. COEFFICIENT10the coefficient for each of the torsional angles=0.00089293
ATOMS11the atoms involved for each of the torsions you wish to calculate=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. COEFFICIENT11the coefficient for each of the torsional angles=-0.23744683
ATOMS12the atoms involved for each of the torsions you wish to calculate=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. COEFFICIENT12the coefficient for each of the torsional angles=0.15661255
ATOMS13the atoms involved for each of the torsions you wish to calculate=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. COEFFICIENT13the coefficient for each of the torsional angles=0.63855605
ATOMS14the atoms involved for each of the torsions you wish to calculate=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. COEFFICIENT14the coefficient for each of the torsional angles=-0.15161411
ATOMS15the atoms involved for each of the torsions you wish to calculate=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. COEFFICIENT15the coefficient for each of the torsional angles=0.50759965
ATOMS16the atoms involved for each of the torsions you wish to calculate=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. COEFFICIENT16the coefficient for each of the torsional angles=-0.04886669
ATOMS17the atoms involved for each of the torsions you wish to calculate=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. COEFFICIENT17the coefficient for each of the torsional angles=0.13599118
ATOMS18the atoms involved for each of the torsions you wish to calculate=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. COEFFICIENT18the coefficient for each of the torsional angles=-0.1007816
...
# ALPHABETA ...
back_torsionsThe TORSION action with label back_torsions calculates the following quantities:| Quantity | Type | Description |
| back_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. ATOMS2the four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. ATOMS3the four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ATOMS4the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ATOMS5the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
back_refThe CONSTANT action with label back_ref calculates the following quantities:| Quantity | Type | Description |
| back_ref | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
back_coeffThe CONSTANT action with label back_coeff calculates the following quantities:| Quantity | Type | Description |
| back_coeff | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.01427455,-0.03003557,-0.23777775,0.139227,0.26525215,-0.18108167,0.01530576,0.07231603,-0.1183752,0.00089293,-0.23744683,0.15661255,0.63855605,-0.15161411,0.50759965,-0.04886669,0.13599118,-0.1007816
back_combThe COMBINE action with label back_comb calculates the following quantities:| Quantity | Type | Description |
| back_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=back_torsions,back_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back_cosThe CUSTOM action with label back_cos calculates the following quantities:| Quantity | Type | Description |
| back_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=back_comb,back_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
backThe SUM action with label back calculates the following quantities:| Quantity | Type | Description |
| back | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=back_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back_torsions: TORSIONCalculate one or multiple torsional angles. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. ATOMS2the four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. ATOMS3the four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ATOMS4the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ATOMS5the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
back_ref: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
back_coeff: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.01427455,-0.03003557,-0.23777775,0.139227,0.26525215,-0.18108167,0.01530576,0.07231603,-0.1183752,0.00089293,-0.23744683,0.15661255,0.63855605,-0.15161411,0.50759965,-0.04886669,0.13599118,-0.1007816
back_comb: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=back_torsions,back_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back_cos: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=back_comb,back_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
back: SUMCalculate the sum of the arguments More details ARGthe values input to this function=back_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
cmapThe CONTACTMAP action with label cmap calculates the following quantities:| Quantity | Type | Description |
| cmap | scalar | the sum of all the switching function on all the distances |
: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.6}
ATOMS1the atoms involved in each of the contacts you wish to calculate=s1,s4 WEIGHT1A weight value for a given contact, by default is 1=0.02521988
ATOMS2the atoms involved in each of the contacts you wish to calculate=s1,s5 WEIGHT2A weight value for a given contact, by default is 1=0.20455216
ATOMS3the atoms involved in each of the contacts you wish to calculate=s1,s6 WEIGHT3A weight value for a given contact, by default is 1=-0.54414755
ATOMS4the atoms involved in each of the contacts you wish to calculate=s1,s7 WEIGHT4A weight value for a given contact, by default is 1=0.36219968
ATOMS5the atoms involved in each of the contacts you wish to calculate=s1,s8 WEIGHT5A weight value for a given contact, by default is 1=0.1279484
ATOMS6the atoms involved in each of the contacts you wish to calculate=s1,s9 WEIGHT6A weight value for a given contact, by default is 1=-0.22453008
ATOMS7the atoms involved in each of the contacts you wish to calculate=s1,s10 WEIGHT7A weight value for a given contact, by default is 1=0.29550159
ATOMS8the atoms involved in each of the contacts you wish to calculate=s2,s5 WEIGHT8A weight value for a given contact, by default is 1=-0.03385588
ATOMS9the atoms involved in each of the contacts you wish to calculate=s2,s6 WEIGHT9A weight value for a given contact, by default is 1=0.09919236
ATOMS10the atoms involved in each of the contacts you wish to calculate=s2,s7 WEIGHT10A weight value for a given contact, by default is 1=-0.03330457
ATOMS11the atoms involved in each of the contacts you wish to calculate=s2,s8 WEIGHT11A weight value for a given contact, by default is 1=-0.13847136
ATOMS12the atoms involved in each of the contacts you wish to calculate=s2,s9 WEIGHT12A weight value for a given contact, by default is 1=0.39094173
ATOMS13the atoms involved in each of the contacts you wish to calculate=s2,s10 WEIGHT13A weight value for a given contact, by default is 1=-0.1983029
ATOMS14the atoms involved in each of the contacts you wish to calculate=s3,s6 WEIGHT14A weight value for a given contact, by default is 1=-0.02328201
ATOMS15the atoms involved in each of the contacts you wish to calculate=s3,s7 WEIGHT15A weight value for a given contact, by default is 1=0.0069981
ATOMS16the atoms involved in each of the contacts you wish to calculate=s3,s8 WEIGHT16A weight value for a given contact, by default is 1=0.2231250
ATOMS17the atoms involved in each of the contacts you wish to calculate=s3,s9 WEIGHT17A weight value for a given contact, by default is 1=-0.25618473
ATOMS18the atoms involved in each of the contacts you wish to calculate=s3,s10 WEIGHT18A weight value for a given contact, by default is 1=0.113674
ATOMS19the atoms involved in each of the contacts you wish to calculate=s4,s7 WEIGHT19A weight value for a given contact, by default is 1=0.01257499
ATOMS20the atoms involved in each of the contacts you wish to calculate=s4,s8 WEIGHT20A weight value for a given contact, by default is 1=-0.01498744
ATOMS21the atoms involved in each of the contacts you wish to calculate=s4,s9 WEIGHT21A weight value for a given contact, by default is 1=-0.11663488
ATOMS22the atoms involved in each of the contacts you wish to calculate=s4,s10 WEIGHT22A weight value for a given contact, by default is 1=0.084924
ATOMS23the atoms involved in each of the contacts you wish to calculate=s5,s8 WEIGHT23A weight value for a given contact, by default is 1=-0.005496
ATOMS24the atoms involved in each of the contacts you wish to calculate=s5,s9 WEIGHT24A weight value for a given contact, by default is 1=0.03150733
ATOMS25the atoms involved in each of the contacts you wish to calculate=s5,s10 WEIGHT25A weight value for a given contact, by default is 1=-0.03456732
ATOMS26the atoms involved in each of the contacts you wish to calculate=s6,s9 WEIGHT26A weight value for a given contact, by default is 1=0.00233215
ATOMS27the atoms involved in each of the contacts you wish to calculate=s6,s10 WEIGHT27A weight value for a given contact, by default is 1=0.01574143
ATOMS28the atoms involved in each of the contacts you wish to calculate=s7,s10 WEIGHT28A weight value for a given contact, by default is 1=-0.01026257
SUM calculate the sum of all the contacts in the input
...
rgThe GYRATION action with label rg calculates the following quantities:| Quantity | Type | Description |
| rg | scalar | the radius of gyration |
: 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=@N-1the N atom in residue 1. Click here for more information. ,@CA-1the CA atom in residue 1. Click here for more information. ,@C-1the C atom in residue 1. Click here for more information. ,@N-2the N atom in residue 2. Click here for more information. ,@CA-2the CA atom in residue 2. Click here for more information. ,@C-2the C atom in residue 2. Click here for more information. ,@N-3the N atom in residue 3. Click here for more information. ,@CA-3the CA atom in residue 3. Click here for more information. ,@C-3the C atom in residue 3. Click here for more information. ,@N-4the N atom in residue 4. Click here for more information. ,@CA-4the CA atom in residue 4. Click here for more information. ,@C-4the C atom in residue 4. Click here for more information. ,@N-5the N atom in residue 5. Click here for more information. ,@CA-5the CA atom in residue 5. Click here for more information. ,@C-5the C atom in residue 5. Click here for more information. ,@N-6the N atom in residue 6. Click here for more information. ,@CA-6the CA atom in residue 6. Click here for more information. ,@C-6the C atom in residue 6. Click here for more information. ,@N-7the N atom in residue 7. Click here for more information. ,@CA-7the CA atom in residue 7. Click here for more information. ,@C-7the C atom in residue 7. Click here for more information. ,@N-8the N atom in residue 8. Click here for more information. ,@CA-8the CA atom in residue 8. Click here for more information. ,@C-8the C atom in residue 8. Click here for more information. ,@N-9the N atom in residue 9. Click here for more information. ,@CA-9the CA atom in residue 9. Click here for more information. ,@C-9the C atom in residue 9. Click here for more information. ,@N-10the N atom in residue 10. Click here for more information. ,@CA-10the CA atom in residue 10. Click here for more information. ,@C-10the C atom in residue 10. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
hhThe ANTIBETARMSD action with label hh calculates the following quantities:| Quantity | Type | Description |
| hh | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 NOPBC ignore the periodic boundary conditions
hh: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 NOPBC ignore the periodic boundary conditions NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=all
# hh: ANTIBETARMSD RESIDUES=all TYPE=DRMSD R_0=0.1 STRANDS_CUTOFF=1 NOPBC
hh_rmsdThe SECONDARY_STRUCTURE_RMSD action with label hh_rmsd calculates the following quantities:| Quantity | Type | Description |
| hh_rmsd | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=1,5,7,22,23,24,26,28,43,44,45,47,49,55,56,57,67,64,69,70,71,73,75,84,85,86,88,90,98,99,100,102,104,105,106,107,109,111,119,120,121,123,125,143,144,145,147,149,164,166 TYPE the manner in which RMSD alignment is performed=DRMSD STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 NOPBC ignore the periodic boundary conditions SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT4this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102
hh_ltThe LESS_THAN action with label hh_lt calculates the following quantities:| Quantity | Type | Description |
| hh_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=hh_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12}
hhThe SUM action with label hh calculates the following quantities:| Quantity | Type | Description |
| hh | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=hh_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
mmThe PBMETAD action with label mm calculates the following quantities:| Quantity | Type | Description |
| mm.bias | scalar | the instantaneous value of the bias potential |
: PBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=back,cmap,rg,hh
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.01,0.001,0.004,0.02
SIGMAthe widths of the Gaussian hills=0.015 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM
GRID_MINthe lower bounds for the grid=-4,-2,0.3,0
GRID_MAXthe upper bounds for the grid=4,2,1.4,3
HEIGHTthe height of the Gaussian hills, one for all biases=0.5 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=10 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
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS.back,../HILLS.cmap,../HILLS.rg,../HILLS.hh
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh
GRID_WSTRIDEfrequency for dumping the grid=10000000
...
SAXSCalculates SAXS intensity. This action has hidden defaults. More details ...
NOPBC Ignore the periodic boundary conditions when calculating distances
LABELa label for the action so that its output can be referenced in the input to other actions=saxsThe SAXS action with label saxs calculates the following quantities:| Quantity | Type | Description |
| saxs.q-0 | scalar | The # SAXS of q This is the 0th of these quantities |
| saxs.q-1 | scalar | The # SAXS of q This is the 1th of these quantities |
| saxs.q-2 | scalar | The # SAXS of q This is the 2th of these quantities |
| saxs.q-3 | scalar | The # SAXS of q This is the 3th of these quantities |
| saxs.q-4 | scalar | The # SAXS of q This is the 4th of these quantities |
| saxs.q-5 | scalar | The # SAXS of q This is the 5th of these quantities |
| saxs.q-6 | scalar | The # SAXS of q This is the 6th of these quantities |
| saxs.q-7 | scalar | The # SAXS of q This is the 7th of these quantities |
| saxs.q-8 | scalar | The # SAXS of q This is the 8th of these quantities |
| saxs.q-9 | scalar | The # SAXS of q This is the 9th of these quantities |
| saxs.q-10 | scalar | The # SAXS of q This is the 10th of these quantities |
| saxs.q-11 | scalar | The # SAXS of q This is the 11th of these quantities |
| saxs.q-12 | scalar | The # SAXS of q This is the 12th of these quantities |
| saxs.q-13 | scalar | The # SAXS of q This is the 13th of these quantities |
| saxs.q-14 | scalar | The # SAXS of q This is the 14th of these quantities |
| saxs.q-15 | scalar | The # SAXS of q This is the 15th of these quantities |
| saxs.q-16 | scalar | The # SAXS of q This is the 16th of these quantities |
| saxs.q-17 | scalar | The # SAXS of q This is the 17th of these quantities |
| saxs.q-18 | scalar | The # SAXS of q This is the 18th of these quantities |
| saxs.q-19 | scalar | The # SAXS of q This is the 19th of these quantities |
| saxs.q-20 | scalar | The # SAXS of q This is the 20th of these quantities |
| saxs.q-21 | scalar | The # SAXS of q This is the 21th of these quantities |
| saxs.q-22 | scalar | The # SAXS of q This is the 22th of these quantities |
| saxs.q-23 | scalar | The # SAXS of q This is the 23th of these quantities |
| saxs.exp-0 | scalar | The # experimental intensity This is the 0th of these quantities |
| saxs.exp-1 | scalar | The # experimental intensity This is the 1th of these quantities |
| saxs.exp-2 | scalar | The # experimental intensity This is the 2th of these quantities |
| saxs.exp-3 | scalar | The # experimental intensity This is the 3th of these quantities |
| saxs.exp-4 | scalar | The # experimental intensity This is the 4th of these quantities |
| saxs.exp-5 | scalar | The # experimental intensity This is the 5th of these quantities |
| saxs.exp-6 | scalar | The # experimental intensity This is the 6th of these quantities |
| saxs.exp-7 | scalar | The # experimental intensity This is the 7th of these quantities |
| saxs.exp-8 | scalar | The # experimental intensity This is the 8th of these quantities |
| saxs.exp-9 | scalar | The # experimental intensity This is the 9th of these quantities |
| saxs.exp-10 | scalar | The # experimental intensity This is the 10th of these quantities |
| saxs.exp-11 | scalar | The # experimental intensity This is the 11th of these quantities |
| saxs.exp-12 | scalar | The # experimental intensity This is the 12th of these quantities |
| saxs.exp-13 | scalar | The # experimental intensity This is the 13th of these quantities |
| saxs.exp-14 | scalar | The # experimental intensity This is the 14th of these quantities |
| saxs.exp-15 | scalar | The # experimental intensity This is the 15th of these quantities |
| saxs.exp-16 | scalar | The # experimental intensity This is the 16th of these quantities |
| saxs.exp-17 | scalar | The # experimental intensity This is the 17th of these quantities |
| saxs.exp-18 | scalar | The # experimental intensity This is the 18th of these quantities |
| saxs.exp-19 | scalar | The # experimental intensity This is the 19th of these quantities |
| saxs.exp-20 | scalar | The # experimental intensity This is the 20th of these quantities |
| saxs.exp-21 | scalar | The # experimental intensity This is the 21th of these quantities |
| saxs.exp-22 | scalar | The # experimental intensity This is the 22th of these quantities |
| saxs.exp-23 | scalar | The # experimental intensity This is the 23th of these quantities |
| saxs.score | scalar | the Metainference score |
| saxs.biasDer | scalar | derivatives with respect to the bias |
| saxs.weight | scalar | weights of the weighted average |
| saxs.neff | scalar | effective number of replicas |
| saxs.scale | scalar | scale parameter |
| saxs.acceptScale | scalar | MC acceptance for scale value |
| saxs.acceptSigma | scalar | MC acceptance for sigma values |
| saxs.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
| saxs.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
| saxs.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
| saxs.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
| saxs.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
| saxs.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
| saxs.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
| saxs.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
| saxs.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
| saxs.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
| saxs.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
| saxs.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
| saxs.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
| saxs.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
| saxs.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
| saxs.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
| saxs.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
| saxs.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
| saxs.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
| saxs.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
| saxs.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
| saxs.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
| saxs.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
| saxs.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
| saxs.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
| saxs.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
| saxs.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
| saxs.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
| saxs.sigmaMean-14 | scalar | uncertainty in the mean estimate This is the 14th of these quantities |
| saxs.sigma-14 | scalar | uncertainty parameter This is the 14th of these quantities |
| saxs.sigmaMean-15 | scalar | uncertainty in the mean estimate This is the 15th of these quantities |
| saxs.sigma-15 | scalar | uncertainty parameter This is the 15th of these quantities |
| saxs.sigmaMean-16 | scalar | uncertainty in the mean estimate This is the 16th of these quantities |
| saxs.sigma-16 | scalar | uncertainty parameter This is the 16th of these quantities |
| saxs.sigmaMean-17 | scalar | uncertainty in the mean estimate This is the 17th of these quantities |
| saxs.sigma-17 | scalar | uncertainty parameter This is the 17th of these quantities |
| saxs.sigmaMean-18 | scalar | uncertainty in the mean estimate This is the 18th of these quantities |
| saxs.sigma-18 | scalar | uncertainty parameter This is the 18th of these quantities |
| saxs.sigmaMean-19 | scalar | uncertainty in the mean estimate This is the 19th of these quantities |
| saxs.sigma-19 | scalar | uncertainty parameter This is the 19th of these quantities |
| saxs.sigmaMean-20 | scalar | uncertainty in the mean estimate This is the 20th of these quantities |
| saxs.sigma-20 | scalar | uncertainty parameter This is the 20th of these quantities |
| saxs.sigmaMean-21 | scalar | uncertainty in the mean estimate This is the 21th of these quantities |
| saxs.sigma-21 | scalar | uncertainty parameter This is the 21th of these quantities |
| saxs.sigmaMean-22 | scalar | uncertainty in the mean estimate This is the 22th of these quantities |
| saxs.sigma-22 | scalar | uncertainty parameter This is the 22th of these quantities |
| saxs.sigmaMean-23 | scalar | uncertainty in the mean estimate This is the 23th of these quantities |
| saxs.sigma-23 | scalar | uncertainty parameter This is the 23th of these quantities |
ATOMSThe atoms to be included in the calculation, e=1-166
ATOMISTIC Calculate SAXS for an atomistic model
SCALE_EXPINT Scaling value for experimental data normalization=100
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.010000 EXPINT1Add an experimental value for each q value=99.884787
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.070000 EXPINT2Add an experimental value for each q value=94.573283
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.130000 EXPINT3Add an experimental value for each q value=82.964898
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.190000 EXPINT4Add an experimental value for each q value=68.296624
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.250000 EXPINT5Add an experimental value for each q value=53.565198
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.310000 EXPINT6Add an experimental value for each q value=40.540191
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.370000 EXPINT7Add an experimental value for each q value=29.869842
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.430000 EXPINT8Add an experimental value for each q value=21.605034
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.490000 EXPINT9Add an experimental value for each q value=15.542217
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.550000 EXPINT10Add an experimental value for each q value=11.346918
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.610000 EXPINT11Add an experimental value for each q value=8.628281
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.670000 EXPINT12Add an experimental value for each q value=7.008095
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.730000 EXPINT13Add an experimental value for each q value=6.154012
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.790000 EXPINT14Add an experimental value for each q value=5.789840
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.850000 EXPINT15Add an experimental value for each q value=5.711048
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.910000 EXPINT16Add an experimental value for each q value=5.799616
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.970000 EXPINT17Add an experimental value for each q value=6.016059
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.030000 EXPINT18Add an experimental value for each q value=6.361548
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.090000 EXPINT19Add an experimental value for each q value=6.825863
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.150000 EXPINT20Add an experimental value for each q value=7.352355
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.210000 EXPINT21Add an experimental value for each q value=7.844432
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.270000 EXPINT22Add an experimental value for each q value=8.208167
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.330000 EXPINT23Add an experimental value for each q value=8.399227
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.390000 EXPINT24Add an experimental value for each q value=8.442345
DOSCORE activate metainference
REWEIGHT simple REWEIGHT using the ARG as energy ARGthe labels of the values from which the function is calculated=mm.bias
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas SCALE_PRIOR either FLAT or GAUSSIAN=FLAT SCALE0 initial value of the scaling factor=1.00 SCALE_MINminimum value of the scaling factor=0.5 SCALE_MAXmaximum value of the scaling factor=1.5 DSCALEmaximum MC move of the scaling factor=0.0002
SIGMA0 initial value of the uncertainty parameter=1
SIGMA_MIN minimum value of the uncertainty parameter=0.001
MC_CHUNKSIZEMC chunksize=2 MC_STEPSnumber of MC steps=12
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=3
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM_MAX
AVERAGINGStride for calculation of averaged weights and sigma_mean=200
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
... SAXS
SAXSCalculates SAXS intensity. This action uses the defaults shown here. More details ...
NOPBC Ignore the periodic boundary conditions when calculating distances
LABELa label for the action so that its output can be referenced in the input to other actions=saxs
ATOMSThe atoms to be included in the calculation, e=1-166
ATOMISTIC Calculate SAXS for an atomistic model
SCALE_EXPINT Scaling value for experimental data normalization=100
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.010000 EXPINT1Add an experimental value for each q value=99.884787
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.070000 EXPINT2Add an experimental value for each q value=94.573283
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.130000 EXPINT3Add an experimental value for each q value=82.964898
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.190000 EXPINT4Add an experimental value for each q value=68.296624
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.250000 EXPINT5Add an experimental value for each q value=53.565198
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.310000 EXPINT6Add an experimental value for each q value=40.540191
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.370000 EXPINT7Add an experimental value for each q value=29.869842
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.430000 EXPINT8Add an experimental value for each q value=21.605034
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.490000 EXPINT9Add an experimental value for each q value=15.542217
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.550000 EXPINT10Add an experimental value for each q value=11.346918
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.610000 EXPINT11Add an experimental value for each q value=8.628281
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.670000 EXPINT12Add an experimental value for each q value=7.008095
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.730000 EXPINT13Add an experimental value for each q value=6.154012
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.790000 EXPINT14Add an experimental value for each q value=5.789840
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.850000 EXPINT15Add an experimental value for each q value=5.711048
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.910000 EXPINT16Add an experimental value for each q value=5.799616
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.970000 EXPINT17Add an experimental value for each q value=6.016059
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.030000 EXPINT18Add an experimental value for each q value=6.361548
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.090000 EXPINT19Add an experimental value for each q value=6.825863
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.150000 EXPINT20Add an experimental value for each q value=7.352355
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.210000 EXPINT21Add an experimental value for each q value=7.844432
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.270000 EXPINT22Add an experimental value for each q value=8.208167
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.330000 EXPINT23Add an experimental value for each q value=8.399227
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =1.390000 EXPINT24Add an experimental value for each q value=8.442345
DOSCORE activate metainference
REWEIGHT simple REWEIGHT using the ARG as energy ARGthe labels of the values from which the function is calculated=mm.bias
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas SCALE_PRIOR either FLAT or GAUSSIAN=FLAT SCALE0 initial value of the scaling factor=1.00 SCALE_MINminimum value of the scaling factor=0.5 SCALE_MAXmaximum value of the scaling factor=1.5 DSCALEmaximum MC move of the scaling factor=0.0002
SIGMA0 initial value of the uncertainty parameter=1
SIGMA_MIN minimum value of the uncertainty parameter=0.001
MC_CHUNKSIZEMC chunksize=2 MC_STEPSnumber of MC steps=12
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=3
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM_MAX
AVERAGINGStride for calculation of averaged weights and sigma_mean=200
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
SIGMA_MAX maximum value of the uncertainty parameter=10. DEVICEID Identifier of the GPU to be used=-1 SOLVDENS Density of the solvent to be used for the correction of atomistic form factors=0.334 SOLVATION_CORRECTION Solvation layer electron density correction (ONEBEAD only)=0.0 SOLVATION_STRIDE Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)=10 SASA_CUTOFF SASA value to consider a residue as exposed to the solvent (ONEBEAD only)=1.0 DEUTER_CONC Fraction of deuterated solvent=0. N Number of points in the resolution function integral=10
... SAXS
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=saxs.score STRIDEthe frequency with which the forces due to the bias should be calculated=2
ensThe ENSEMBLE action with label ens calculates the following quantities:| Quantity | Type | Description |
| ens.saxs.q-0 | scalar | the average for argument saxs.q-0 |
| ens.saxs.q-1 | scalar | the average for argument saxs.q-1 |
| ens.saxs.q-2 | scalar | the average for argument saxs.q-2 |
| ens.saxs.q-3 | scalar | the average for argument saxs.q-3 |
| ens.saxs.q-4 | scalar | the average for argument saxs.q-4 |
| ens.saxs.q-5 | scalar | the average for argument saxs.q-5 |
| ens.saxs.q-6 | scalar | the average for argument saxs.q-6 |
| ens.saxs.q-7 | scalar | the average for argument saxs.q-7 |
| ens.saxs.q-8 | scalar | the average for argument saxs.q-8 |
| ens.saxs.q-9 | scalar | the average for argument saxs.q-9 |
| ens.saxs.q-10 | scalar | the average for argument saxs.q-10 |
| ens.saxs.q-11 | scalar | the average for argument saxs.q-11 |
| ens.saxs.q-12 | scalar | the average for argument saxs.q-12 |
| ens.saxs.q-13 | scalar | the average for argument saxs.q-13 |
| ens.saxs.q-14 | scalar | the average for argument saxs.q-14 |
| ens.saxs.q-15 | scalar | the average for argument saxs.q-15 |
| ens.saxs.q-16 | scalar | the average for argument saxs.q-16 |
| ens.saxs.q-17 | scalar | the average for argument saxs.q-17 |
| ens.saxs.q-18 | scalar | the average for argument saxs.q-18 |
| ens.saxs.q-19 | scalar | the average for argument saxs.q-19 |
| ens.saxs.q-20 | scalar | the average for argument saxs.q-20 |
| ens.saxs.q-21 | scalar | the average for argument saxs.q-21 |
| ens.saxs.q-22 | scalar | the average for argument saxs.q-22 |
| ens.saxs.q-23 | scalar | the average for argument saxs.q-23 |
: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(saxs\.q-.*),mm.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
stThe STATS action with label st calculates the following quantities:| Quantity | Type | Description |
| st.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
| st.corr | scalar | the correlation between arguments and parameters |
| st.slope | scalar | the slope of a linear fit between arguments and parameters |
| st.intercept | scalar | the intercept of a linear fit between arguments and parameters |
: 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=(ens\.saxs\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxs\.exp-.*)
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxs\.score),(saxs\.biasDer),(saxs\.weight),(saxs\.neff),(saxs\.scale),(saxs\.acceptScale),(saxs\.acceptSigma),(saxs\.sigma.*) FILEthe name of the file on which to output these quantities=BAYES STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=st.*,(ens\.saxs\.q-.*) FILEthe name of the file on which to output these quantities=STATS STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=back,cmap,rg,hh FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=5000
