Project ID: plumID:23.029
Source: UP1_RNA/SLC_OFF/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
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_AA.pdb
The MOLINFO action with label calculates somethingproteinThe GROUP action with label protein calculates the following quantities:| Quantity | Type | Description |
| protein | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-3124
rnaThe GROUP action with label rna calculates the following quantities:| Quantity | Type | Description |
| rna | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3125-3511
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=rna AROUNDreference atoms=protein
cPHE20The CENTER_FAST action with label cPHE20 calculates the following quantities:| Quantity | Type | Description |
| cPHE20 | 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=@CG-20the CG atom in residue 20. Click here for more information. ,@CD1-20the CD1 atom in residue 20. Click here for more information. ,@CE1-20the CE1 atom in residue 20. Click here for more information. ,@CZ-20the CZ atom in residue 20. Click here for more information. ,@CE2-20the CE2 atom in residue 20. Click here for more information. ,@CD2-20the CD2 atom in residue 20. Click here for more information.
cPHE62The CENTER_FAST action with label cPHE62 calculates the following quantities:| Quantity | Type | Description |
| cPHE62 | 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=@CG-62the CG atom in residue 62. Click here for more information. ,@CD1-62the CD1 atom in residue 62. Click here for more information. ,@CE1-62the CE1 atom in residue 62. Click here for more information. ,@CZ-62the CZ atom in residue 62. Click here for more information. ,@CE2-62the CE2 atom in residue 62. Click here for more information. ,@CD2-62the CD2 atom in residue 62. Click here for more information.
cPHE111The CENTER_FAST action with label cPHE111 calculates the following quantities:| Quantity | Type | Description |
| cPHE111 | 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=@CG-111the CG atom in residue 111. Click here for more information. ,@CD1-111the CD1 atom in residue 111. Click here for more information. ,@CE1-111the CE1 atom in residue 111. Click here for more information. ,@CZ-111the CZ atom in residue 111. Click here for more information. ,@CE2-111the CE2 atom in residue 111. Click here for more information. ,@CD2-111the CD2 atom in residue 111. Click here for more information.
cPHE153The CENTER_FAST action with label cPHE153 calculates the following quantities:| Quantity | Type | Description |
| cPHE153 | 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=@CG-153the CG atom in residue 153. Click here for more information. ,@CD1-153the CD1 atom in residue 153. Click here for more information. ,@CE1-153the CE1 atom in residue 153. Click here for more information. ,@CZ-153the CZ atom in residue 153. Click here for more information. ,@CE2-153the CE2 atom in residue 153. Click here for more information. ,@CD2-153the CD2 atom in residue 153. Click here for more information.
cA4The CENTER_FAST action with label cA4 calculates the following quantities:| Quantity | Type | Description |
| cA4 | 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=@N1-203the N1 atom in residue 203. Click here for more information. ,@C2-203the C2 atom in residue 203. Click here for more information. ,@N3-203the N3 atom in residue 203. Click here for more information. ,@C4-203the C4 atom in residue 203. Click here for more information. ,@C5-203the C5 atom in residue 203. Click here for more information. ,@C6-203the C6 atom in residue 203. Click here for more information. ,@N7-203the N7 atom in residue 203. Click here for more information. ,@C8-203the C8 atom in residue 203. Click here for more information. ,@N9-203the N9 atom in residue 203. Click here for more information.
cG5The CENTER_FAST action with label cG5 calculates the following quantities:| Quantity | Type | Description |
| cG5 | 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=@N1-204the N1 atom in residue 204. Click here for more information. ,@C2-204the C2 atom in residue 204. Click here for more information. ,@N3-204the N3 atom in residue 204. Click here for more information. ,@C4-204the C4 atom in residue 204. Click here for more information. ,@C5-204the C5 atom in residue 204. Click here for more information. ,@C6-204the C6 atom in residue 204. Click here for more information. ,@N7-204the N7 atom in residue 204. Click here for more information. ,@C8-204the C8 atom in residue 204. Click here for more information. ,@N9-204the N9 atom in residue 204. Click here for more information.
cA9The CENTER_FAST action with label cA9 calculates the following quantities:| Quantity | Type | Description |
| cA9 | 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=@N1-208the N1 atom in residue 208. Click here for more information. ,@C2-208the C2 atom in residue 208. Click here for more information. ,@N3-208the N3 atom in residue 208. Click here for more information. ,@C4-208the C4 atom in residue 208. Click here for more information. ,@C5-208the C5 atom in residue 208. Click here for more information. ,@C6-208the C6 atom in residue 208. Click here for more information. ,@N7-208the N7 atom in residue 208. Click here for more information. ,@C8-208the C8 atom in residue 208. Click here for more information. ,@N9-208the N9 atom in residue 208. Click here for more information.
cG10The CENTER_FAST action with label cG10 calculates the following quantities:| Quantity | Type | Description |
| cG10 | 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=@N1-209the N1 atom in residue 209. Click here for more information. ,@C2-209the C2 atom in residue 209. Click here for more information. ,@N3-209the N3 atom in residue 209. Click here for more information. ,@C4-209the C4 atom in residue 209. Click here for more information. ,@C5-209the C5 atom in residue 209. Click here for more information. ,@C6-209the C6 atom in residue 209. Click here for more information. ,@N7-209the N7 atom in residue 209. Click here for more information. ,@C8-209the C8 atom in residue 209. Click here for more information. ,@N9-209the N9 atom in residue 209. Click here for more information.
ring1The DISTANCE action with label ring1 calculates the following quantities:| Quantity | Type | Description |
| ring1 | 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=cPHE20,cA4
ring2The DISTANCE action with label ring2 calculates the following quantities:| Quantity | Type | Description |
| ring2 | 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=cPHE62,cG5
ring3The DISTANCE action with label ring3 calculates the following quantities:| Quantity | Type | Description |
| ring3 | 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=cPHE111,cA9
ring4The DISTANCE action with label ring4 calculates the following quantities:| Quantity | Type | Description |
| ring4 | 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=cPHE153,cG10
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=ring1,ring2,ring3,ring4 ATthe positions of the wall=0.35,0.35,0.35,0.35 KAPPAthe force constant for the wall=1000.0,1000.0,1000.0,1000.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_ringThe UPPER_WALLS action with label uwall_ring calculates the following quantities:| Quantity | Type | Description |
| uwall_ring.bias | scalar | the instantaneous value of the bias potential |
| uwall_ring.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
sb1The DISTANCE action with label sb1 calculates the following quantities:| Quantity | Type | Description |
| sb1 | 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=@CZ-78the CZ atom in residue 78. Click here for more information. ,@CG-158the CG atom in residue 158. Click here for more information.
sb2The DISTANCE action with label sb2 calculates the following quantities:| Quantity | Type | Description |
| sb2 | 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=@CZ-91the CZ atom in residue 91. Click here for more information. ,@CG-160the CG atom in residue 160. Click here for more information.
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=sb1,sb2 ATthe positions of the wall=0.4,0.4 KAPPAthe force constant for the wall=1000.0,1000.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_sbThe UPPER_WALLS action with label uwall_sb calculates the following quantities:| Quantity | Type | Description |
| uwall_sb.bias | scalar | the instantaneous value of the bias potential |
| uwall_sb.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
a1The RMSD action with label a1 calculates the following quantities:| Quantity | Type | Description |
| a1 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a2The RMSD action with label a2 calculates the following quantities:| Quantity | Type | Description |
| a2 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a3The RMSD action with label a3 calculates the following quantities:| Quantity | Type | Description |
| a3 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a4The RMSD action with label a4 calculates the following quantities:| Quantity | Type | Description |
| a4 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a4: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a5The RMSD action with label a5 calculates the following quantities:| Quantity | Type | Description |
| a5 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha5.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a5: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha5.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a6The RMSD action with label a6 calculates the following quantities:| Quantity | Type | Description |
| a6 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha6.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a6: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha6.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a7The RMSD action with label a7 calculates the following quantities:| Quantity | Type | Description |
| a7 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha7.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a7: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha7.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a8The RMSD action with label a8 calculates the following quantities:| Quantity | Type | Description |
| a8 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha8.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a8: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha8.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
a9The RMSD action with label a9 calculates the following quantities:| Quantity | Type | Description |
| a9 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha9.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
a9: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=alpha9.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
b1The RMSD action with label b1 calculates the following quantities:| Quantity | Type | Description |
| b1 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
b1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
b2The RMSD action with label b2 calculates the following quantities:| Quantity | Type | Description |
| b2 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
b2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
b3The RMSD action with label b3 calculates the following quantities:| Quantity | Type | Description |
| b3 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
b3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
b4The RMSD action with label b4 calculates the following quantities:| Quantity | Type | Description |
| b4 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
b4: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=beta4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 ATthe positions of the wall=0,0,0,0,0,0,0,0,0,0,0,0,0 KAPPAthe force constant for the wall=10000.0,10000.0,10000.0,10000.0,10000.0,20000.0,10000.0,10000.0,10000.0,10000.0,20000.0,10000.0,10000.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_ssThe UPPER_WALLS action with label uwall_ss calculates the following quantities:| Quantity | Type | Description |
| uwall_ss.bias | scalar | the instantaneous value of the bias potential |
| uwall_ss.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
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=saxsdataThe SAXS action with label saxsdata calculates the following quantities:| Quantity | Type | Description |
| saxsdata.q-0 | scalar | The # SAXS of q This is the 0th of these quantities |
| saxsdata.q-1 | scalar | The # SAXS of q This is the 1th of these quantities |
| saxsdata.q-2 | scalar | The # SAXS of q This is the 2th of these quantities |
| saxsdata.q-3 | scalar | The # SAXS of q This is the 3th of these quantities |
| saxsdata.q-4 | scalar | The # SAXS of q This is the 4th of these quantities |
| saxsdata.q-5 | scalar | The # SAXS of q This is the 5th of these quantities |
| saxsdata.q-6 | scalar | The # SAXS of q This is the 6th of these quantities |
| saxsdata.q-7 | scalar | The # SAXS of q This is the 7th of these quantities |
| saxsdata.q-8 | scalar | The # SAXS of q This is the 8th of these quantities |
| saxsdata.q-9 | scalar | The # SAXS of q This is the 9th of these quantities |
| saxsdata.q-10 | scalar | The # SAXS of q This is the 10th of these quantities |
| saxsdata.q-11 | scalar | The # SAXS of q This is the 11th of these quantities |
| saxsdata.q-12 | scalar | The # SAXS of q This is the 12th of these quantities |
| saxsdata.q-13 | scalar | The # SAXS of q This is the 13th of these quantities |
| saxsdata.q-14 | scalar | The # SAXS of q This is the 14th of these quantities |
| saxsdata.q-15 | scalar | The # SAXS of q This is the 15th of these quantities |
| saxsdata.q-16 | scalar | The # SAXS of q This is the 16th of these quantities |
| saxsdata.q-17 | scalar | The # SAXS of q This is the 17th of these quantities |
| saxsdata.q-18 | scalar | The # SAXS of q This is the 18th of these quantities |
| saxsdata.q-19 | scalar | The # SAXS of q This is the 19th of these quantities |
| saxsdata.q-20 | scalar | The # SAXS of q This is the 20th of these quantities |
| saxsdata.q-21 | scalar | The # SAXS of q This is the 21th of these quantities |
| saxsdata.q-22 | scalar | The # SAXS of q This is the 22th of these quantities |
| saxsdata.q-23 | scalar | The # SAXS of q This is the 23th of these quantities |
| saxsdata.q-24 | scalar | The # SAXS of q This is the 24th of these quantities |
| saxsdata.q-25 | scalar | The # SAXS of q This is the 25th of these quantities |
| saxsdata.q-26 | scalar | The # SAXS of q This is the 26th of these quantities |
| saxsdata.q-27 | scalar | The # SAXS of q This is the 27th of these quantities |
| saxsdata.q-28 | scalar | The # SAXS of q This is the 28th of these quantities |
| saxsdata.q-29 | scalar | The # SAXS of q This is the 29th of these quantities |
| saxsdata.q-30 | scalar | The # SAXS of q This is the 30th of these quantities |
| saxsdata.q-31 | scalar | The # SAXS of q This is the 31th of these quantities |
| saxsdata.q-32 | scalar | The # SAXS of q This is the 32th of these quantities |
| saxsdata.q-33 | scalar | The # SAXS of q This is the 33th of these quantities |
| saxsdata.q-34 | scalar | The # SAXS of q This is the 34th of these quantities |
| saxsdata.exp-0 | scalar | The # experimental intensity This is the 0th of these quantities |
| saxsdata.exp-1 | scalar | The # experimental intensity This is the 1th of these quantities |
| saxsdata.exp-2 | scalar | The # experimental intensity This is the 2th of these quantities |
| saxsdata.exp-3 | scalar | The # experimental intensity This is the 3th of these quantities |
| saxsdata.exp-4 | scalar | The # experimental intensity This is the 4th of these quantities |
| saxsdata.exp-5 | scalar | The # experimental intensity This is the 5th of these quantities |
| saxsdata.exp-6 | scalar | The # experimental intensity This is the 6th of these quantities |
| saxsdata.exp-7 | scalar | The # experimental intensity This is the 7th of these quantities |
| saxsdata.exp-8 | scalar | The # experimental intensity This is the 8th of these quantities |
| saxsdata.exp-9 | scalar | The # experimental intensity This is the 9th of these quantities |
| saxsdata.exp-10 | scalar | The # experimental intensity This is the 10th of these quantities |
| saxsdata.exp-11 | scalar | The # experimental intensity This is the 11th of these quantities |
| saxsdata.exp-12 | scalar | The # experimental intensity This is the 12th of these quantities |
| saxsdata.exp-13 | scalar | The # experimental intensity This is the 13th of these quantities |
| saxsdata.exp-14 | scalar | The # experimental intensity This is the 14th of these quantities |
| saxsdata.exp-15 | scalar | The # experimental intensity This is the 15th of these quantities |
| saxsdata.exp-16 | scalar | The # experimental intensity This is the 16th of these quantities |
| saxsdata.exp-17 | scalar | The # experimental intensity This is the 17th of these quantities |
| saxsdata.exp-18 | scalar | The # experimental intensity This is the 18th of these quantities |
| saxsdata.exp-19 | scalar | The # experimental intensity This is the 19th of these quantities |
| saxsdata.exp-20 | scalar | The # experimental intensity This is the 20th of these quantities |
| saxsdata.exp-21 | scalar | The # experimental intensity This is the 21th of these quantities |
| saxsdata.exp-22 | scalar | The # experimental intensity This is the 22th of these quantities |
| saxsdata.exp-23 | scalar | The # experimental intensity This is the 23th of these quantities |
| saxsdata.exp-24 | scalar | The # experimental intensity This is the 24th of these quantities |
| saxsdata.exp-25 | scalar | The # experimental intensity This is the 25th of these quantities |
| saxsdata.exp-26 | scalar | The # experimental intensity This is the 26th of these quantities |
| saxsdata.exp-27 | scalar | The # experimental intensity This is the 27th of these quantities |
| saxsdata.exp-28 | scalar | The # experimental intensity This is the 28th of these quantities |
| saxsdata.exp-29 | scalar | The # experimental intensity This is the 29th of these quantities |
| saxsdata.exp-30 | scalar | The # experimental intensity This is the 30th of these quantities |
| saxsdata.exp-31 | scalar | The # experimental intensity This is the 31th of these quantities |
| saxsdata.exp-32 | scalar | The # experimental intensity This is the 32th of these quantities |
| saxsdata.exp-33 | scalar | The # experimental intensity This is the 33th of these quantities |
| saxsdata.exp-34 | scalar | The # experimental intensity This is the 34th of these quantities |
| saxsdata.score | scalar | the Metainference score |
| saxsdata.neff | scalar | effective number of replicas |
| saxsdata.scale | scalar | scale parameter |
| saxsdata.acceptScale | scalar | MC acceptance for scale value |
| saxsdata.acceptSigma | scalar | MC acceptance for sigma values |
| saxsdata.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
| saxsdata.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
| saxsdata.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
| saxsdata.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
| saxsdata.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
| saxsdata.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
| saxsdata.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
| saxsdata.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
| saxsdata.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
| saxsdata.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
| saxsdata.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
| saxsdata.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
| saxsdata.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
| saxsdata.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
| saxsdata.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
| saxsdata.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
| saxsdata.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
| saxsdata.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
| saxsdata.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
| saxsdata.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
| saxsdata.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
| saxsdata.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
| saxsdata.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
| saxsdata.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
| saxsdata.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
| saxsdata.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
| saxsdata.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
| saxsdata.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
| saxsdata.sigmaMean-14 | scalar | uncertainty in the mean estimate This is the 14th of these quantities |
| saxsdata.sigma-14 | scalar | uncertainty parameter This is the 14th of these quantities |
| saxsdata.sigmaMean-15 | scalar | uncertainty in the mean estimate This is the 15th of these quantities |
| saxsdata.sigma-15 | scalar | uncertainty parameter This is the 15th of these quantities |
| saxsdata.sigmaMean-16 | scalar | uncertainty in the mean estimate This is the 16th of these quantities |
| saxsdata.sigma-16 | scalar | uncertainty parameter This is the 16th of these quantities |
| saxsdata.sigmaMean-17 | scalar | uncertainty in the mean estimate This is the 17th of these quantities |
| saxsdata.sigma-17 | scalar | uncertainty parameter This is the 17th of these quantities |
| saxsdata.sigmaMean-18 | scalar | uncertainty in the mean estimate This is the 18th of these quantities |
| saxsdata.sigma-18 | scalar | uncertainty parameter This is the 18th of these quantities |
| saxsdata.sigmaMean-19 | scalar | uncertainty in the mean estimate This is the 19th of these quantities |
| saxsdata.sigma-19 | scalar | uncertainty parameter This is the 19th of these quantities |
| saxsdata.sigmaMean-20 | scalar | uncertainty in the mean estimate This is the 20th of these quantities |
| saxsdata.sigma-20 | scalar | uncertainty parameter This is the 20th of these quantities |
| saxsdata.sigmaMean-21 | scalar | uncertainty in the mean estimate This is the 21th of these quantities |
| saxsdata.sigma-21 | scalar | uncertainty parameter This is the 21th of these quantities |
| saxsdata.sigmaMean-22 | scalar | uncertainty in the mean estimate This is the 22th of these quantities |
| saxsdata.sigma-22 | scalar | uncertainty parameter This is the 22th of these quantities |
| saxsdata.sigmaMean-23 | scalar | uncertainty in the mean estimate This is the 23th of these quantities |
| saxsdata.sigma-23 | scalar | uncertainty parameter This is the 23th of these quantities |
| saxsdata.sigmaMean-24 | scalar | uncertainty in the mean estimate This is the 24th of these quantities |
| saxsdata.sigma-24 | scalar | uncertainty parameter This is the 24th of these quantities |
| saxsdata.sigmaMean-25 | scalar | uncertainty in the mean estimate This is the 25th of these quantities |
| saxsdata.sigma-25 | scalar | uncertainty parameter This is the 25th of these quantities |
| saxsdata.sigmaMean-26 | scalar | uncertainty in the mean estimate This is the 26th of these quantities |
| saxsdata.sigma-26 | scalar | uncertainty parameter This is the 26th of these quantities |
| saxsdata.sigmaMean-27 | scalar | uncertainty in the mean estimate This is the 27th of these quantities |
| saxsdata.sigma-27 | scalar | uncertainty parameter This is the 27th of these quantities |
| saxsdata.sigmaMean-28 | scalar | uncertainty in the mean estimate This is the 28th of these quantities |
| saxsdata.sigma-28 | scalar | uncertainty parameter This is the 28th of these quantities |
| saxsdata.sigmaMean-29 | scalar | uncertainty in the mean estimate This is the 29th of these quantities |
| saxsdata.sigma-29 | scalar | uncertainty parameter This is the 29th of these quantities |
| saxsdata.sigmaMean-30 | scalar | uncertainty in the mean estimate This is the 30th of these quantities |
| saxsdata.sigma-30 | scalar | uncertainty parameter This is the 30th of these quantities |
| saxsdata.sigmaMean-31 | scalar | uncertainty in the mean estimate This is the 31th of these quantities |
| saxsdata.sigma-31 | scalar | uncertainty parameter This is the 31th of these quantities |
| saxsdata.sigmaMean-32 | scalar | uncertainty in the mean estimate This is the 32th of these quantities |
| saxsdata.sigma-32 | scalar | uncertainty parameter This is the 32th of these quantities |
| saxsdata.sigmaMean-33 | scalar | uncertainty in the mean estimate This is the 33th of these quantities |
| saxsdata.sigma-33 | scalar | uncertainty parameter This is the 33th of these quantities |
| saxsdata.sigmaMean-34 | scalar | uncertainty in the mean estimate This is the 34th of these quantities |
| saxsdata.sigma-34 | scalar | uncertainty parameter This is the 34th of these quantities |
ATOMSThe atoms to be included in the calculation, e=1-3511
ONEBEAD calculate SAXS for a single bead model
TEMPLATE A PDB file is required for ONEBEAD mapping=template_AA.pdb
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)=0.000
SCALE_EXPINT Scaling value for experimental data normalization=0.201148E+01
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.839003E-02 EXPINT1Add an experimental value for each q value=0.198653E+01
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.167801E-01 EXPINT2Add an experimental value for each q value=0.191350E+01
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.251701E-01 EXPINT3Add an experimental value for each q value=0.179763E+01
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.337520E-01 EXPINT4Add an experimental value for each q value=0.164327E+01
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.423340E-01 EXPINT5Add an experimental value for each q value=0.146336E+01
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.509160E-01 EXPINT6Add an experimental value for each q value=0.126966E+01
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.594979E-01 EXPINT7Add an experimental value for each q value=0.107369E+01
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.680799E-01 EXPINT8Add an experimental value for each q value=0.885614E+00
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.766619E-01 EXPINT9Add an experimental value for each q value=0.713508E+00
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.852438E-01 EXPINT10Add an experimental value for each q value=0.562829E+00
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.938258E-01 EXPINT11Add an experimental value for each q value=0.436336E+00
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.102408E+00 EXPINT12Add an experimental value for each q value=0.334334E+00
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.110990E+00 EXPINT13Add an experimental value for each q value=0.255154E+00
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.119572E+00 EXPINT14Add an experimental value for each q value=0.195774E+00
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.128154E+00 EXPINT15Add an experimental value for each q value=0.152481E+00
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.136736E+00 EXPINT16Add an experimental value for each q value=0.121461E+00
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.145318E+00 EXPINT17Add an experimental value for each q value=0.992440E-01
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.153900E+00 EXPINT18Add an experimental value for each q value=0.829832E-01
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162482E+00 EXPINT19Add an experimental value for each q value=0.705616E-01
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.171064E+00 EXPINT20Add an experimental value for each q value=0.605595E-01
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.179645E+00 EXPINT21Add an experimental value for each q value=0.521321E-01
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.188227E+00 EXPINT22Add an experimental value for each q value=0.448387E-01
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196809E+00 EXPINT23Add an experimental value for each q value=0.384860E-01
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.205391E+00 EXPINT24Add an experimental value for each q value=0.329934E-01
QVALUE25Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.213973E+00 EXPINT25Add an experimental value for each q value=0.283112E-01
QVALUE26Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.222555E+00 EXPINT26Add an experimental value for each q value=0.243814E-01
QVALUE27Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.231137E+00 EXPINT27Add an experimental value for each q value=0.211332E-01
QVALUE28Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.239719E+00 EXPINT28Add an experimental value for each q value=0.184941E-01
QVALUE29Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.248301E+00 EXPINT29Add an experimental value for each q value=0.164044E-01
QVALUE30Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.256883E+00 EXPINT30Add an experimental value for each q value=0.148225E-01
QVALUE31Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.265465E+00 EXPINT31Add an experimental value for each q value=0.137188E-01
QVALUE32Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.274047E+00 EXPINT32Add an experimental value for each q value=0.130615E-01
QVALUE33Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.282629E+00 EXPINT33Add an experimental value for each q value=0.128002E-01
QVALUE34Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.291211E+00 EXPINT34Add an experimental value for each q value=0.128542E-01
QVALUE35Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.299793E+00 EXPINT35Add an experimental value for each q value=0.131114E-01
DOSCORE activate metainference
NOENSEMBLE don't perform any replica-averaging
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0
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=GAUSSIAN SCALE0 initial value of the scaling factor=1.00 DSCALEmaximum MC move of the scaling factor=0.001
SIGMA0 initial value of the uncertainty parameter=0.1
SIGMA_MAX maximum value of the uncertainty parameter=0.1
SIGMA_MIN minimum value of the uncertainty parameter=0.00001
DSIGMAmaximum MC move of the uncertainty parameter=0.0005
MC_STEPSnumber of MC steps=35 MC_CHUNKSIZEMC chunksize=1
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=1000
... 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=saxsdata
ATOMSThe atoms to be included in the calculation, e=1-3511
ONEBEAD calculate SAXS for a single bead model
TEMPLATE A PDB file is required for ONEBEAD mapping=template_AA.pdb
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)=0.000
SCALE_EXPINT Scaling value for experimental data normalization=0.201148E+01
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.839003E-02 EXPINT1Add an experimental value for each q value=0.198653E+01
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.167801E-01 EXPINT2Add an experimental value for each q value=0.191350E+01
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.251701E-01 EXPINT3Add an experimental value for each q value=0.179763E+01
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.337520E-01 EXPINT4Add an experimental value for each q value=0.164327E+01
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.423340E-01 EXPINT5Add an experimental value for each q value=0.146336E+01
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.509160E-01 EXPINT6Add an experimental value for each q value=0.126966E+01
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.594979E-01 EXPINT7Add an experimental value for each q value=0.107369E+01
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.680799E-01 EXPINT8Add an experimental value for each q value=0.885614E+00
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.766619E-01 EXPINT9Add an experimental value for each q value=0.713508E+00
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.852438E-01 EXPINT10Add an experimental value for each q value=0.562829E+00
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.938258E-01 EXPINT11Add an experimental value for each q value=0.436336E+00
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.102408E+00 EXPINT12Add an experimental value for each q value=0.334334E+00
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.110990E+00 EXPINT13Add an experimental value for each q value=0.255154E+00
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.119572E+00 EXPINT14Add an experimental value for each q value=0.195774E+00
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.128154E+00 EXPINT15Add an experimental value for each q value=0.152481E+00
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.136736E+00 EXPINT16Add an experimental value for each q value=0.121461E+00
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.145318E+00 EXPINT17Add an experimental value for each q value=0.992440E-01
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.153900E+00 EXPINT18Add an experimental value for each q value=0.829832E-01
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162482E+00 EXPINT19Add an experimental value for each q value=0.705616E-01
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.171064E+00 EXPINT20Add an experimental value for each q value=0.605595E-01
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.179645E+00 EXPINT21Add an experimental value for each q value=0.521321E-01
QVALUE22Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.188227E+00 EXPINT22Add an experimental value for each q value=0.448387E-01
QVALUE23Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196809E+00 EXPINT23Add an experimental value for each q value=0.384860E-01
QVALUE24Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.205391E+00 EXPINT24Add an experimental value for each q value=0.329934E-01
QVALUE25Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.213973E+00 EXPINT25Add an experimental value for each q value=0.283112E-01
QVALUE26Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.222555E+00 EXPINT26Add an experimental value for each q value=0.243814E-01
QVALUE27Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.231137E+00 EXPINT27Add an experimental value for each q value=0.211332E-01
QVALUE28Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.239719E+00 EXPINT28Add an experimental value for each q value=0.184941E-01
QVALUE29Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.248301E+00 EXPINT29Add an experimental value for each q value=0.164044E-01
QVALUE30Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.256883E+00 EXPINT30Add an experimental value for each q value=0.148225E-01
QVALUE31Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.265465E+00 EXPINT31Add an experimental value for each q value=0.137188E-01
QVALUE32Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.274047E+00 EXPINT32Add an experimental value for each q value=0.130615E-01
QVALUE33Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.282629E+00 EXPINT33Add an experimental value for each q value=0.128002E-01
QVALUE34Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.291211E+00 EXPINT34Add an experimental value for each q value=0.128542E-01
QVALUE35Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.299793E+00 EXPINT35Add an experimental value for each q value=0.131114E-01
DOSCORE activate metainference
NOENSEMBLE don't perform any replica-averaging
SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0
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=GAUSSIAN SCALE0 initial value of the scaling factor=1.00 DSCALEmaximum MC move of the scaling factor=0.001
SIGMA0 initial value of the uncertainty parameter=0.1
SIGMA_MAX maximum value of the uncertainty parameter=0.1
SIGMA_MIN minimum value of the uncertainty parameter=0.00001
DSIGMAmaximum MC move of the uncertainty parameter=0.0005
MC_STEPSnumber of MC steps=35 MC_CHUNKSIZEMC chunksize=1
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=1000
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE DEVICEID Identifier of the GPU to be used=-1 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
saxsbiasThe BIASVALUE action with label saxsbias calculates the following quantities:| Quantity | Type | Description |
| saxsbias.bias | scalar | the instantaneous value of the bias potential |
| saxsbias.saxsdata.score_bias | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named saxsdata.score |
: 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=(saxsdata\.score) STRIDEthe frequency with which the forces due to the bias should be calculated=1
statcgThe STATS action with label statcg calculates the following quantities:| Quantity | Type | Description |
| statcg.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
| statcg.corr | scalar | the correlation between arguments and parameters |
| statcg.slope | scalar | the slope of a linear fit between arguments and parameters |
| statcg.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=(saxsdata\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsdata\.exp-.*)
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=ring1,ring2,ring3,ring4,sb1,sb2 FILEthe name of the file on which to output these quantities=DISTANCES
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=a1,a2,a3,a4,a5,a6,a7,a8,a9,b1,b2,b3,b4 FILEthe name of the file on which to output these quantities=RMSDSS
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=uwall_ring.bias,uwall_sb.bias,uwall_ss.bias FILEthe name of the file on which to output these quantities=RESTRAINTS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=SAXSINT
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=statcg.* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=ST.SAXSCG
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.score),(saxsdata\.scale),(saxsdata\.acceptScale),(saxsdata\.acceptSigma),(saxsdata\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=BAYES.SAXS
