Project ID: plumID:20.009
Source: Ub3/plumed-cv.dat
Originally used with PLUMED version: 2.6
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=1-489
aThe CENTER_FAST action with label a calculates the following quantities:| Quantity | Type | Description |
| a | 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=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150 NOPBC ignore the periodic boundary conditions when calculating distances
a1The CENTER_FAST action with label a1 calculates the following quantities:| Quantity | Type | Description |
| a1 | 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=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75 NOPBC ignore the periodic boundary conditions when calculating distances
a2The CENTER_FAST action with label a2 calculates the following quantities:| Quantity | Type | Description |
| a2 | 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=77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150 NOPBC ignore the periodic boundary conditions when calculating distances
bThe CENTER_FAST action with label b calculates the following quantities:| Quantity | Type | Description |
| b | 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=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313 NOPBC ignore the periodic boundary conditions when calculating distances
b1The CENTER_FAST action with label b1 calculates the following quantities:| Quantity | Type | Description |
| b1 | 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=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238 NOPBC ignore the periodic boundary conditions when calculating distances
b2The CENTER_FAST action with label b2 calculates the following quantities:| Quantity | Type | Description |
| b2 | 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=,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313 NOPBC ignore the periodic boundary conditions when calculating distances
cThe CENTER_FAST action with label c calculates the following quantities:| Quantity | Type | Description |
| c | 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=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476 NOPBC ignore the periodic boundary conditions when calculating distances
c1The CENTER_FAST action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | 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=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401 NOPBC ignore the periodic boundary conditions when calculating distances
c2The CENTER_FAST action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | 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=403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476 NOPBC ignore the periodic boundary conditions when calculating distances
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,b NOPBC ignore the periodic boundary conditions when calculating distances
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,c NOPBC ignore the periodic boundary conditions when calculating distances
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=b,c NOPBC ignore the periodic boundary conditions when calculating distances
tor1The TORSION action with label tor1 calculates the following quantities:| Quantity | Type | Description |
| tor1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,b1,b2 NOPBC ignore the periodic boundary conditions when calculating distances
tor2The TORSION action with label tor2 calculates the following quantities:| Quantity | Type | Description |
| tor2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,c1,c2 NOPBC ignore the periodic boundary conditions when calculating distances
tor3The TORSION action with label tor3 calculates the following quantities:| Quantity | Type | Description |
| tor3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=b1,b2,c1,c2 NOPBC ignore the periodic boundary conditions when calculating distances
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=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150,152,154,157,159,162,163,164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313,315,317,320,322,325,326,327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476,478,480,483,485,488,489 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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor1The ALPHABETA action with label linktor1 calculates the following quantities:| Quantity | Type | Description |
| linktor1 | 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=150,152,154,157
ATOMS2the atoms involved for each of the torsions you wish to calculate=152,154,157,159
ATOMS3the atoms involved for each of the torsions you wish to calculate=154,157,159,162
ATOMS4the atoms involved for each of the torsions you wish to calculate=157,159,162,163
ATOMS5the atoms involved for each of the torsions you wish to calculate=159,162,163,164
ATOMS6the atoms involved for each of the torsions you wish to calculate=162,163,164,166
... ALPHABETA
# ALPHABETA ...
linktor1_torsionsThe TORSION action with label linktor1_torsions calculates the following quantities:| Quantity | Type | Description |
| linktor1_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=150,152,154,157 ATOMS2the four atoms involved in the torsional angle=152,154,157,159 ATOMS3the four atoms involved in the torsional angle=154,157,159,162 ATOMS4the four atoms involved in the torsional angle=157,159,162,163 ATOMS5the four atoms involved in the torsional angle=159,162,163,164
linktor1_refThe CONSTANT action with label linktor1_ref calculates the following quantities:| Quantity | Type | Description |
| linktor1_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
linktor1_coeffThe CONSTANT action with label linktor1_coeff calculates the following quantities:| Quantity | Type | Description |
| linktor1_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=1,1,1,1,1,1
linktor1_combThe COMBINE action with label linktor1_comb calculates the following quantities:| Quantity | Type | Description |
| linktor1_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=linktor1_torsions,linktor1_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
linktor1_cosThe CUSTOM action with label linktor1_cos calculates the following quantities:| Quantity | Type | Description |
| linktor1_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=linktor1_comb,linktor1_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
linktor1The SUM action with label linktor1 calculates the following quantities:| Quantity | Type | Description |
| linktor1 | 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=linktor1_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor2The ALPHABETA action with label linktor2 calculates the following quantities:| Quantity | Type | Description |
| linktor2 | 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=313,315,317,320
ATOMS2the atoms involved for each of the torsions you wish to calculate=315,317,320,322
ATOMS3the atoms involved for each of the torsions you wish to calculate=317,320,322,325
ATOMS4the atoms involved for each of the torsions you wish to calculate=320,322,325,326
ATOMS5the atoms involved for each of the torsions you wish to calculate=322,325,326,327
ATOMS6the atoms involved for each of the torsions you wish to calculate=325,326,327,329
... ALPHABETA
# ALPHABETA ...
linktor2_torsionsThe TORSION action with label linktor2_torsions calculates the following quantities:| Quantity | Type | Description |
| linktor2_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=313,315,317,320 ATOMS2the four atoms involved in the torsional angle=315,317,320,322 ATOMS3the four atoms involved in the torsional angle=317,320,322,325 ATOMS4the four atoms involved in the torsional angle=320,322,325,326 ATOMS5the four atoms involved in the torsional angle=322,325,326,327
linktor2_refThe CONSTANT action with label linktor2_ref calculates the following quantities:| Quantity | Type | Description |
| linktor2_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
linktor2_coeffThe CONSTANT action with label linktor2_coeff calculates the following quantities:| Quantity | Type | Description |
| linktor2_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=1,1,1,1,1,1
linktor2_combThe COMBINE action with label linktor2_comb calculates the following quantities:| Quantity | Type | Description |
| linktor2_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=linktor2_torsions,linktor2_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
linktor2_cosThe CUSTOM action with label linktor2_cos calculates the following quantities:| Quantity | Type | Description |
| linktor2_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=linktor2_comb,linktor2_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
linktor2The SUM action with label linktor2 calculates the following quantities:| Quantity | Type | Description |
| linktor2 | 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=linktor2_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
SAXSCalculates SAXS intensity. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=test2The SAXS action with label test2 calculates the following quantities:| Quantity | Type | Description |
| test2.q-0 | scalar | The # SAXS of q This is the 0th of these quantities |
| test2.q-1 | scalar | The # SAXS of q This is the 1th of these quantities |
| test2.q-2 | scalar | The # SAXS of q This is the 2th of these quantities |
| test2.q-3 | scalar | The # SAXS of q This is the 3th of these quantities |
| test2.q-4 | scalar | The # SAXS of q This is the 4th of these quantities |
| test2.q-5 | scalar | The # SAXS of q This is the 5th of these quantities |
| test2.q-6 | scalar | The # SAXS of q This is the 6th of these quantities |
| test2.q-7 | scalar | The # SAXS of q This is the 7th of these quantities |
| test2.q-8 | scalar | The # SAXS of q This is the 8th of these quantities |
| test2.q-9 | scalar | The # SAXS of q This is the 9th of these quantities |
| test2.q-10 | scalar | The # SAXS of q This is the 10th of these quantities |
| test2.q-11 | scalar | The # SAXS of q This is the 11th of these quantities |
| test2.q-12 | scalar | The # SAXS of q This is the 12th of these quantities |
| test2.q-13 | scalar | The # SAXS of q This is the 13th of these quantities |
| test2.q-14 | scalar | The # SAXS of q This is the 14th of these quantities |
| test2.q-15 | scalar | The # SAXS of q This is the 15th of these quantities |
| test2.q-16 | scalar | The # SAXS of q This is the 16th of these quantities |
| test2.q-17 | scalar | The # SAXS of q This is the 17th of these quantities |
| test2.q-18 | scalar | The # SAXS of q This is the 18th of these quantities |
| test2.q-19 | scalar | The # SAXS of q This is the 19th of these quantities |
| test2.q-20 | scalar | The # SAXS of q This is the 20th of these quantities |
| test2.exp-0 | scalar | The # experimental intensity This is the 0th of these quantities |
| test2.exp-1 | scalar | The # experimental intensity This is the 1th of these quantities |
| test2.exp-2 | scalar | The # experimental intensity This is the 2th of these quantities |
| test2.exp-3 | scalar | The # experimental intensity This is the 3th of these quantities |
| test2.exp-4 | scalar | The # experimental intensity This is the 4th of these quantities |
| test2.exp-5 | scalar | The # experimental intensity This is the 5th of these quantities |
| test2.exp-6 | scalar | The # experimental intensity This is the 6th of these quantities |
| test2.exp-7 | scalar | The # experimental intensity This is the 7th of these quantities |
| test2.exp-8 | scalar | The # experimental intensity This is the 8th of these quantities |
| test2.exp-9 | scalar | The # experimental intensity This is the 9th of these quantities |
| test2.exp-10 | scalar | The # experimental intensity This is the 10th of these quantities |
| test2.exp-11 | scalar | The # experimental intensity This is the 11th of these quantities |
| test2.exp-12 | scalar | The # experimental intensity This is the 12th of these quantities |
| test2.exp-13 | scalar | The # experimental intensity This is the 13th of these quantities |
| test2.exp-14 | scalar | The # experimental intensity This is the 14th of these quantities |
| test2.exp-15 | scalar | The # experimental intensity This is the 15th of these quantities |
| test2.exp-16 | scalar | The # experimental intensity This is the 16th of these quantities |
| test2.exp-17 | scalar | The # experimental intensity This is the 17th of these quantities |
| test2.exp-18 | scalar | The # experimental intensity This is the 18th of these quantities |
| test2.exp-19 | scalar | The # experimental intensity This is the 19th of these quantities |
| test2.exp-20 | scalar | The # experimental intensity This is the 20th of these quantities |
ATOMSThe atoms to be included in the calculation, e=1-489
NOPBC Ignore the periodic boundary conditions when calculating distances
MARTINI Calculate SAXS for a Martini model
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0178612
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.029015
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0401689
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0513227
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0624766
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0736304
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0847843
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0959381
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.107092
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.118246
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.129399
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.140553
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.151707
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162861
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.174015
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.185169
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196323
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.207476
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.21863
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.229784
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.240938
EXPINT1Add an experimental value for each q value=4.68143
EXPINT2Add an experimental value for each q value=4.11699
EXPINT3Add an experimental value for each q value=3.45783
EXPINT4Add an experimental value for each q value=2.76077
EXPINT5Add an experimental value for each q value=2.15094
EXPINT6Add an experimental value for each q value=1.67643
EXPINT7Add an experimental value for each q value=1.32305
EXPINT8Add an experimental value for each q value=1.06339
EXPINT9Add an experimental value for each q value=0.870742
EXPINT10Add an experimental value for each q value=0.721004
EXPINT11Add an experimental value for each q value=0.597613
EXPINT12Add an experimental value for each q value=0.493722
EXPINT13Add an experimental value for each q value=0.407671
EXPINT14Add an experimental value for each q value=0.337263
EXPINT15Add an experimental value for each q value=0.27869
EXPINT16Add an experimental value for each q value=0.228546
EXPINT17Add an experimental value for each q value=0.184443
EXPINT18Add an experimental value for each q value=0.144056
EXPINT19Add an experimental value for each q value=0.106039
EXPINT20Add an experimental value for each q value=0.0725692
EXPINT21Add an experimental value for each q value=0.0480033
... SAXS
SAXSCalculates SAXS intensity. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=test2
ATOMSThe atoms to be included in the calculation, e=1-489
NOPBC Ignore the periodic boundary conditions when calculating distances
MARTINI Calculate SAXS for a Martini model
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0178612
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.029015
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0401689
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0513227
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0624766
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0736304
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0847843
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0959381
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.107092
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.118246
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.129399
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.140553
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.151707
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162861
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.174015
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.185169
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196323
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.207476
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.21863
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.229784
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.240938
EXPINT1Add an experimental value for each q value=4.68143
EXPINT2Add an experimental value for each q value=4.11699
EXPINT3Add an experimental value for each q value=3.45783
EXPINT4Add an experimental value for each q value=2.76077
EXPINT5Add an experimental value for each q value=2.15094
EXPINT6Add an experimental value for each q value=1.67643
EXPINT7Add an experimental value for each q value=1.32305
EXPINT8Add an experimental value for each q value=1.06339
EXPINT9Add an experimental value for each q value=0.870742
EXPINT10Add an experimental value for each q value=0.721004
EXPINT11Add an experimental value for each q value=0.597613
EXPINT12Add an experimental value for each q value=0.493722
EXPINT13Add an experimental value for each q value=0.407671
EXPINT14Add an experimental value for each q value=0.337263
EXPINT15Add an experimental value for each q value=0.27869
EXPINT16Add an experimental value for each q value=0.228546
EXPINT17Add an experimental value for each q value=0.184443
EXPINT18Add an experimental value for each q value=0.144056
EXPINT19Add an experimental value for each q value=0.106039
EXPINT20Add an experimental value for each q value=0.0725692
EXPINT21Add an experimental value for each q value=0.0480033
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0 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 SCALE_EXPINT Scaling value for experimental data normalization=1.0 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
lsaxsThe STATS action with label lsaxs calculates the following quantities:| Quantity | Type | Description |
| lsaxs.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
| lsaxs.corr | scalar | the correlation between arguments and parameters |
| lsaxs.slope | scalar | the slope of a linear fit between arguments and parameters |
| lsaxs.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=(test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)
PBMETADUsed 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=biasThe PBMETAD action with label bias calculates the following quantities:| Quantity | Type | Description |
| bias.bias | scalar | the instantaneous value of the bias potential |
ARGthe labels of the scalars on which the bias will act=d1,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2
HEIGHTthe height of the Gaussian hills, one for all biases=0.1
PACEthe frequency for hill addition, one for all biases=200
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=30
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID.0,GRID.1,GRID.2,GRID.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8
GRID_WSTRIDEfrequency for dumping the grid=2000
SIGMAthe widths of the Gaussian hills=10000
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2
GRID_MINthe lower bounds for the grid=0,0,0,-pi,-pi,-pi,0,0,0
GRID_MAXthe upper bounds for the grid=7,14,7,pi,pi,pi,7,6,6
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
UPDATE_FROMOnly update this action from this time=10000
... PBMETAD
METAINFERENCECalculates 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=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(test2\.exp-.*)
SCALE_PRIOR either FLAT or GAUSSIAN=FLAT
ADDOFFSET Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_PRIOR either FLAT or GAUSSIAN=FLAT
OFFSET0 initial value of the offset=0 OFFSET_MINminimum value of the offset=-10 OFFSET_MAXmaximum value of the offset=10 DOFFSETmaximum MC move of the offset=0.005
SCALE0 initial value of the scaling factor=1.00 SCALE_MINminimum value of the scaling factor=0.8 SCALE_MAXmaximum value of the scaling factor=1.2 DSCALEmaximum MC move of the scaling factor=0.001
SIGMA0 initial value of the uncertainty parameter=0.01 SIGMA_MIN minimum value of the uncertainty parameter=0. SIGMA_MAX maximum value of the uncertainty parameter=0.05
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=bqThe METAINFERENCE action with label bq calculates the following quantities:| Quantity | Type | Description |
| bq.bias | scalar | the instantaneous value of the bias potential |
| bq.biasDer | scalar | derivatives with respect to the bias |
| bq.weight | scalar | weights of the weighted average |
| bq.neff | scalar | effective number of replicas |
| bq.scale | scalar | scale parameter |
| bq.offset | scalar | offset parameter |
| bq.acceptScale | scalar | MC acceptance for scale value |
| bq.acceptSigma | scalar | MC acceptance for sigma values |
| bq.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
| bq.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
| bq.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
| bq.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
| bq.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
| bq.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
| bq.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
| bq.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
| bq.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
| bq.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
| bq.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
| bq.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
| bq.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
| bq.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
| bq.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
| bq.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
| bq.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
| bq.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
| bq.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
| bq.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
| bq.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
| bq.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
| bq.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
| bq.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
| bq.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
| bq.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
| bq.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
| bq.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
| bq.sigmaMean-14 | scalar | uncertainty in the mean estimate This is the 14th of these quantities |
| bq.sigma-14 | scalar | uncertainty parameter This is the 14th of these quantities |
| bq.sigmaMean-15 | scalar | uncertainty in the mean estimate This is the 15th of these quantities |
| bq.sigma-15 | scalar | uncertainty parameter This is the 15th of these quantities |
| bq.sigmaMean-16 | scalar | uncertainty in the mean estimate This is the 16th of these quantities |
| bq.sigma-16 | scalar | uncertainty parameter This is the 16th of these quantities |
| bq.sigmaMean-17 | scalar | uncertainty in the mean estimate This is the 17th of these quantities |
| bq.sigma-17 | scalar | uncertainty parameter This is the 17th of these quantities |
| bq.sigmaMean-18 | scalar | uncertainty in the mean estimate This is the 18th of these quantities |
| bq.sigma-18 | scalar | uncertainty parameter This is the 18th of these quantities |
| bq.sigmaMean-19 | scalar | uncertainty in the mean estimate This is the 19th of these quantities |
| bq.sigma-19 | scalar | uncertainty parameter This is the 19th of these quantities |
| bq.sigmaMean-20 | scalar | uncertainty in the mean estimate This is the 20th of these quantities |
| bq.sigma-20 | scalar | uncertainty parameter This is the 20th of these quantities |
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=5
... METAINFERENCE
ensaxsThe ENSEMBLE action with label ensaxs calculates the following quantities:| Quantity | Type | Description |
| ensaxs.test2.q-0 | scalar | the average for argument test2.q-0 |
| ensaxs.test2.q-1 | scalar | the average for argument test2.q-1 |
| ensaxs.test2.q-2 | scalar | the average for argument test2.q-2 |
| ensaxs.test2.q-3 | scalar | the average for argument test2.q-3 |
| ensaxs.test2.q-4 | scalar | the average for argument test2.q-4 |
| ensaxs.test2.q-5 | scalar | the average for argument test2.q-5 |
| ensaxs.test2.q-6 | scalar | the average for argument test2.q-6 |
| ensaxs.test2.q-7 | scalar | the average for argument test2.q-7 |
| ensaxs.test2.q-8 | scalar | the average for argument test2.q-8 |
| ensaxs.test2.q-9 | scalar | the average for argument test2.q-9 |
| ensaxs.test2.q-10 | scalar | the average for argument test2.q-10 |
| ensaxs.test2.q-11 | scalar | the average for argument test2.q-11 |
| ensaxs.test2.q-12 | scalar | the average for argument test2.q-12 |
| ensaxs.test2.q-13 | scalar | the average for argument test2.q-13 |
| ensaxs.test2.q-14 | scalar | the average for argument test2.q-14 |
| ensaxs.test2.q-15 | scalar | the average for argument test2.q-15 |
| ensaxs.test2.q-16 | scalar | the average for argument test2.q-16 |
| ensaxs.test2.q-17 | scalar | the average for argument test2.q-17 |
| ensaxs.test2.q-18 | scalar | the average for argument test2.q-18 |
| ensaxs.test2.q-19 | scalar | the average for argument test2.q-19 |
| ensaxs.test2.q-20 | scalar | the average for argument test2.q-20 |
: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
statsqThe STATS action with label statsq calculates the following quantities:| Quantity | Type | Description |
| statsq.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
| statsq.corr | scalar | the correlation between arguments and parameters |
| statsq.slope | scalar | the slope of a linear fit between arguments and parameters |
| statsq.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=(ensaxs\.test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)
enANAThe ENSEMBLE action with label enANA calculates the following quantities:| Quantity | Type | Description |
| enANA.d1 | scalar | the average for argument d1 |
| enANA.d2 | scalar | the average for argument d2 |
| enANA.d3 | scalar | the average for argument d3 |
| enANA.tor1 | scalar | the average for argument tor1 |
| enANA.tor2 | scalar | the average for argument tor2 |
| enANA.tor3 | scalar | the average for argument tor3 |
| enANA.rg | scalar | the average for argument rg |
| enANA.linktor1 | scalar | the average for argument linktor1 |
| enANA.linktor2 | scalar | the average for argument linktor2 |
: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=d1,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2,bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(test2\.q-.*),(test2\.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=bq.* 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=d1,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2 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\.test2\.q-.*) 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=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
