Project ID: plumID:19.025
Source: run-c22/plumed.dat
Originally used with PLUMED version: 2.4
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
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein 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=1-111
psi1The TORSION action with label psi1 calculates the following quantities: Quantity | Type | Description |
psi1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi2The TORSION action with label psi2 calculates the following quantities: Quantity | Type | Description |
psi2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi3The TORSION action with label psi3 calculates the following quantities: Quantity | Type | Description |
psi3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi4The TORSION action with label psi4 calculates the following quantities: Quantity | Type | Description |
psi4 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi5The TORSION action with label psi5 calculates the following quantities: Quantity | Type | Description |
psi5 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi6The TORSION action with label psi6 calculates the following quantities: Quantity | Type | Description |
psi6 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi7The TORSION action with label psi7 calculates the following quantities: Quantity | Type | Description |
psi7 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
psi8The TORSION action with label psi8 calculates the following quantities: Quantity | Type | Description |
psi8 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi2The TORSION action with label phi2 calculates the following quantities: Quantity | Type | Description |
phi2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi3The TORSION action with label phi3 calculates the following quantities: Quantity | Type | Description |
phi3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi4The TORSION action with label phi4 calculates the following quantities: Quantity | Type | Description |
phi4 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi5The TORSION action with label phi5 calculates the following quantities: Quantity | Type | Description |
phi5 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi6The TORSION action with label phi6 calculates the following quantities: Quantity | Type | Description |
phi6 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi7The TORSION action with label phi7 calculates the following quantities: Quantity | Type | Description |
phi7 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi8The TORSION action with label phi8 calculates the following quantities: Quantity | Type | Description |
phi8 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
phi9The TORSION action with label phi9 calculates the following quantities: Quantity | Type | Description |
phi9 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
dihtrp_cacbThe TORSION action with label dihtrp_cacb calculates the following quantities: Quantity | Type | Description |
dihtrp_cacb | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=67,47,49,52
dihtrp_cbcgThe TORSION action with label dihtrp_cbcg calculates the following quantities: Quantity | Type | Description |
dihtrp_cbcg | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=47,49,52,53
gyrThe GYRATION action with label gyr calculates the following quantities: Quantity | Type | Description |
gyr | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@CA-1the CA atom in residue 1. Click here for more information. ,@CA-2the CA atom in residue 2. Click here for more information. ,@CA-3the CA atom in residue 3. Click here for more information. ,@CA-4the CA atom in residue 4. Click here for more information. ,@CA-5the CA atom in residue 5. Click here for more information. ,@CA-6the CA atom in residue 6. Click here for more information. ,@CA-7the CA atom in residue 7. Click here for more information. ,@CA-8the CA atom in residue 8. Click here for more information. ,@CA-9the CA atom in residue 9. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
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=pbThe PBMETAD action with label pb calculates the following quantities: Quantity | Type | Description |
pb.bias | scalar | the instantaneous value of the bias potential |
ARGthe labels of the scalars on which the bias will act=phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg
SIGMAthe widths of the Gaussian hills=1000
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
HEIGHTthe height of the Gaussian hills, one for all biases=0.5
PACEthe frequency for hill addition, one for all biases=200
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=34
GRID_MINthe lower bounds for the grid=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
GRID_WSTRIDEfrequency for dumping the grid=50000
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... PBMETAD
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=gyr,phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg STRIDE the frequency with which the quantities of interest should be output=2000
RDCCalculates the (Residual) Dipolar Coupling between two atoms. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
GYROM Add the product of the gyromagnetic constants for the bond=-72.5388
SCALE Add the scaling factor to take into account concentration and other effects=0.001
ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=18,19 COUPLING1Add an experimental value for each coupling (needed by SVD and useful for STATS)=-5.4
ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=25,26 COUPLING2Add an experimental value for each coupling (needed by SVD and useful for STATS)=-1.26
ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=35,36 COUPLING3Add an experimental value for each coupling (needed by SVD and useful for STATS)=-5.22
ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=45,46 COUPLING4Add an experimental value for each coupling (needed by SVD and useful for STATS)=-0.91
ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=69,70 COUPLING5Add an experimental value for each coupling (needed by SVD and useful for STATS)=2.33
ATOMS6the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=79,80 COUPLING6Add an experimental value for each coupling (needed by SVD and useful for STATS)=-2.88
ATOMS7the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=89,90 COUPLING7Add an experimental value for each coupling (needed by SVD and useful for STATS)=-8.37
ATOMS8the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=100,101 COUPLING8Add an experimental value for each coupling (needed by SVD and useful for STATS)=-3.78
LABELa label for the action so that its output can be referenced in the input to other actions=nhThe RDC action with label nh calculates the following quantities: Quantity | Type | Description |
nh.rdc-0 | scalar | the calculated # RDC This is the 0th of these quantities |
nh.rdc-1 | scalar | the calculated # RDC This is the 1th of these quantities |
nh.rdc-2 | scalar | the calculated # RDC This is the 2th of these quantities |
nh.rdc-3 | scalar | the calculated # RDC This is the 3th of these quantities |
nh.rdc-4 | scalar | the calculated # RDC This is the 4th of these quantities |
nh.rdc-5 | scalar | the calculated # RDC This is the 5th of these quantities |
nh.rdc-6 | scalar | the calculated # RDC This is the 6th of these quantities |
nh.rdc-7 | scalar | the calculated # RDC This is the 7th of these quantities |
nh.exp-0 | scalar | the experimental # RDC This is the 0th of these quantities |
nh.exp-1 | scalar | the experimental # RDC This is the 1th of these quantities |
nh.exp-2 | scalar | the experimental # RDC This is the 2th of these quantities |
nh.exp-3 | scalar | the experimental # RDC This is the 3th of these quantities |
nh.exp-4 | scalar | the experimental # RDC This is the 4th of these quantities |
nh.exp-5 | scalar | the experimental # RDC This is the 5th of these quantities |
nh.exp-6 | scalar | the experimental # RDC This is the 6th of these quantities |
nh.exp-7 | scalar | the experimental # RDC This is the 7th of these quantities |
nh.score | scalar | the Metainference score |
nh.biasDer | scalar | derivatives with respect to the bias |
nh.weight | scalar | weights of the weighted average |
nh.neff | scalar | effective number of replicas |
nh.scale | scalar | scale parameter |
nh.acceptSigma | scalar | MC acceptance for sigma values |
nh.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
nh.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
nh.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
nh.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
nh.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
nh.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
nh.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
nh.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
nh.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
nh.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
nh.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
nh.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
nh.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
nh.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
nh.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
nh.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
DOSCORE activate metainference
ARGthe labels of the values from which the function is calculated=pb.bias
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS REWEIGHT simple REWEIGHT using the ARG as energy OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=200
REGRES_ZEROstride for regression with zero offset=200
SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=5.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
... RDC
mnhThe BIASVALUE action with label mnh calculates the following quantities: Quantity | Type | Description |
mnh.bias | scalar | the instantaneous value of the bias potential |
mnh.nh.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 nh.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=nh.score
RDCCalculates the (Residual) Dipolar Coupling between two atoms. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
GYROM Add the product of the gyromagnetic constants for the bond=179.9319
SCALE Add the scaling factor to take into account concentration and other effects=0.001
ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=5,6 COUPLING1Add an experimental value for each coupling (needed by SVD and useful for STATS)=12.95
ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=27,28 COUPLING2Add an experimental value for each coupling (needed by SVD and useful for STATS)=11.5
ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=37,38 COUPLING3Add an experimental value for each coupling (needed by SVD and useful for STATS)=21.42
ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=47,48 COUPLING4Add an experimental value for each coupling (needed by SVD and useful for STATS)=-9.37
ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=71,72 COUPLING5Add an experimental value for each coupling (needed by SVD and useful for STATS)=10.01
ATOMS6the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=81,82 COUPLING6Add an experimental value for each coupling (needed by SVD and useful for STATS)=15.01
ATOMS7the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=91,92 COUPLING7Add an experimental value for each coupling (needed by SVD and useful for STATS)=15.73
LABELa label for the action so that its output can be referenced in the input to other actions=cahaThe RDC action with label caha calculates the following quantities: Quantity | Type | Description |
caha.rdc-0 | scalar | the calculated # RDC This is the 0th of these quantities |
caha.rdc-1 | scalar | the calculated # RDC This is the 1th of these quantities |
caha.rdc-2 | scalar | the calculated # RDC This is the 2th of these quantities |
caha.rdc-3 | scalar | the calculated # RDC This is the 3th of these quantities |
caha.rdc-4 | scalar | the calculated # RDC This is the 4th of these quantities |
caha.rdc-5 | scalar | the calculated # RDC This is the 5th of these quantities |
caha.rdc-6 | scalar | the calculated # RDC This is the 6th of these quantities |
caha.exp-0 | scalar | the experimental # RDC This is the 0th of these quantities |
caha.exp-1 | scalar | the experimental # RDC This is the 1th of these quantities |
caha.exp-2 | scalar | the experimental # RDC This is the 2th of these quantities |
caha.exp-3 | scalar | the experimental # RDC This is the 3th of these quantities |
caha.exp-4 | scalar | the experimental # RDC This is the 4th of these quantities |
caha.exp-5 | scalar | the experimental # RDC This is the 5th of these quantities |
caha.exp-6 | scalar | the experimental # RDC This is the 6th of these quantities |
caha.score | scalar | the Metainference score |
caha.biasDer | scalar | derivatives with respect to the bias |
caha.weight | scalar | weights of the weighted average |
caha.neff | scalar | effective number of replicas |
caha.scale | scalar | scale parameter |
caha.acceptSigma | scalar | MC acceptance for sigma values |
caha.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
caha.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
caha.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
caha.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
caha.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
caha.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
caha.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
caha.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
caha.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
caha.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
caha.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
caha.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
caha.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
caha.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
DOSCORE activate metainference
ARGthe labels of the values from which the function is calculated=pb.bias
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS REWEIGHT simple REWEIGHT using the ARG as energy OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=200
REGRES_ZEROstride for regression with zero offset=200
SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=5.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
... RDC
mcahaThe BIASVALUE action with label mcaha calculates the following quantities: Quantity | Type | Description |
mcaha.bias | scalar | the instantaneous value of the bias potential |
mcaha.caha.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 caha.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=caha.score
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=HAN
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. COUPLING1Add an experimental value for each coupling=-0.49
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. COUPLING2Add an experimental value for each coupling=-0.54
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. COUPLING3Add an experimental value for each coupling=-0.53
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. COUPLING4Add an experimental value for each coupling=-0.39
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. COUPLING5Add an experimental value for each coupling=-0.39
LABELa label for the action so that its output can be referenced in the input to other actions=jhanThe JCOUPLING action with label jhan calculates the following quantities: Quantity | Type | Description |
jhan.j-0 | scalar | the calculated J-coupling This is the 0th of these quantities |
jhan.j-1 | scalar | the calculated J-coupling This is the 1th of these quantities |
jhan.j-2 | scalar | the calculated J-coupling This is the 2th of these quantities |
jhan.j-3 | scalar | the calculated J-coupling This is the 3th of these quantities |
jhan.j-4 | scalar | the calculated J-coupling This is the 4th of these quantities |
jhan.exp-0 | scalar | the experimental J-coupling This is the 0th of these quantities |
jhan.exp-1 | scalar | the experimental J-coupling This is the 1th of these quantities |
jhan.exp-2 | scalar | the experimental J-coupling This is the 2th of these quantities |
jhan.exp-3 | scalar | the experimental J-coupling This is the 3th of these quantities |
jhan.exp-4 | scalar | the experimental J-coupling This is the 4th of these quantities |
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=HAN
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. COUPLING1Add an experimental value for each coupling=-0.49
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. COUPLING2Add an experimental value for each coupling=-0.54
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. COUPLING3Add an experimental value for each coupling=-0.53
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. COUPLING4Add an experimental value for each coupling=-0.39
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. COUPLING5Add an experimental value for each coupling=-0.39
LABELa label for the action so that its output can be referenced in the input to other actions=jhan
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.
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=HAHN
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. COUPLING1Add an experimental value for each coupling=6.05
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. COUPLING2Add an experimental value for each coupling=5.95
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. COUPLING3Add an experimental value for each coupling=6.44
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. COUPLING4Add an experimental value for each coupling=6.53
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. COUPLING5Add an experimental value for each coupling=5.93
ATOMS6the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. COUPLING6Add an experimental value for each coupling=6.98
ATOMS7the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. COUPLING7Add an experimental value for each coupling=7.16
LABELa label for the action so that its output can be referenced in the input to other actions=jhahnThe JCOUPLING action with label jhahn calculates the following quantities: Quantity | Type | Description |
jhahn.j-0 | scalar | the calculated J-coupling This is the 0th of these quantities |
jhahn.j-1 | scalar | the calculated J-coupling This is the 1th of these quantities |
jhahn.j-2 | scalar | the calculated J-coupling This is the 2th of these quantities |
jhahn.j-3 | scalar | the calculated J-coupling This is the 3th of these quantities |
jhahn.j-4 | scalar | the calculated J-coupling This is the 4th of these quantities |
jhahn.j-5 | scalar | the calculated J-coupling This is the 5th of these quantities |
jhahn.j-6 | scalar | the calculated J-coupling This is the 6th of these quantities |
jhahn.exp-0 | scalar | the experimental J-coupling This is the 0th of these quantities |
jhahn.exp-1 | scalar | the experimental J-coupling This is the 1th of these quantities |
jhahn.exp-2 | scalar | the experimental J-coupling This is the 2th of these quantities |
jhahn.exp-3 | scalar | the experimental J-coupling This is the 3th of these quantities |
jhahn.exp-4 | scalar | the experimental J-coupling This is the 4th of these quantities |
jhahn.exp-5 | scalar | the experimental J-coupling This is the 5th of these quantities |
jhahn.exp-6 | scalar | the experimental J-coupling This is the 6th of these quantities |
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=HAHN
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. COUPLING1Add an experimental value for each coupling=6.05
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. COUPLING2Add an experimental value for each coupling=5.95
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. COUPLING3Add an experimental value for each coupling=6.44
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. COUPLING4Add an experimental value for each coupling=6.53
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. COUPLING5Add an experimental value for each coupling=5.93
ATOMS6the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. COUPLING6Add an experimental value for each coupling=6.98
ATOMS7the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. COUPLING7Add an experimental value for each coupling=7.16
LABELa label for the action so that its output can be referenced in the input to other actions=jhahn
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.
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=CCG
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@chi1-5the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. COUPLING1Add an experimental value for each coupling=1.59
LABELa label for the action so that its output can be referenced in the input to other actions=jccgThe JCOUPLING action with label jccg calculates the following quantities: Quantity | Type | Description |
jccg.j-0 | scalar | the calculated J-coupling This is the 0th of these quantities |
jccg.exp-0 | scalar | the experimental J-coupling This is the 0th of these quantities |
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=CCG
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@chi1-5the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. COUPLING1Add an experimental value for each coupling=1.59
LABELa label for the action so that its output can be referenced in the input to other actions=jccg
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.
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=NCG
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@chi1-5the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. COUPLING1Add an experimental value for each coupling=1.21
LABELa label for the action so that its output can be referenced in the input to other actions=jncgThe JCOUPLING action with label jncg calculates the following quantities: Quantity | Type | Description |
jncg.j-0 | scalar | the calculated J-coupling This is the 0th of these quantities |
jncg.exp-0 | scalar | the experimental J-coupling This is the 0th of these quantities |
... JCOUPLING
JCOUPLINGCalculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details ...
NOPBC ignore the periodic boundary conditions when calculating distances
TYPEType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)=NCG
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling=@chi1-5the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. COUPLING1Add an experimental value for each coupling=1.21
LABELa label for the action so that its output can be referenced in the input to other actions=jncg
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.
... JCOUPLING
METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ...
ARGthe labels of the scalars on which the bias will act=(jhan\.j-.*),(jhahn\.j-.*),(jccg\.j.*),(jncg\.j.*),pb.bias
PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(jhan\.exp-.*),(jhahn\.exp-.*),(jccg\.exp.*),(jncg\.exp.*)
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=200
SIGMA0 initial value of the uncertainty parameter=2.5 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=5.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
LABELa label for the action so that its output can be referenced in the input to other actions=byjThe METAINFERENCE action with label byj calculates the following quantities: Quantity | Type | Description |
byj.bias | scalar | the instantaneous value of the bias potential |
byj.biasDer | scalar | derivatives with respect to the bias |
byj.weight | scalar | weights of the weighted average |
byj.neff | scalar | effective number of replicas |
byj.acceptSigma | scalar | MC acceptance for sigma values |
byj.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
byj.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
byj.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
byj.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
byj.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
byj.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
byj.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
byj.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
byj.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
byj.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
byj.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
byj.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
byj.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
byj.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
byj.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
byj.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
byj.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
byj.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
byj.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
byj.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
byj.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
byj.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
byj.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
byj.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
byj.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
byj.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
byj.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
byj.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
... METAINFERENCE
csThe CS2BACKBONE action with label cs calculates the following quantities: Quantity | Type | Description |
cs.ca-0-2 | scalar | the calculated Ca carbon chemical shifts This is the 0-2th of these quantities |
cs.ca-0-3 | scalar | the calculated Ca carbon chemical shifts This is the 0-3th of these quantities |
cs.ca-0-4 | scalar | the calculated Ca carbon chemical shifts This is the 0-4th of these quantities |
cs.ca-0-5 | scalar | the calculated Ca carbon chemical shifts This is the 0-5th of these quantities |
cs.ca-0-6 | scalar | the calculated Ca carbon chemical shifts This is the 0-6th of these quantities |
cs.ca-0-7 | scalar | the calculated Ca carbon chemical shifts This is the 0-7th of these quantities |
cs.ca-0-8 | scalar | the calculated Ca carbon chemical shifts This is the 0-8th of these quantities |
cs.cb-0-3 | scalar | the calculated Cb carbon chemical shifts This is the 0-3th of these quantities |
cs.cb-0-4 | scalar | the calculated Cb carbon chemical shifts This is the 0-4th of these quantities |
cs.cb-0-5 | scalar | the calculated Cb carbon chemical shifts This is the 0-5th of these quantities |
cs.cb-0-6 | scalar | the calculated Cb carbon chemical shifts This is the 0-6th of these quantities |
cs.cb-0-7 | scalar | the calculated Cb carbon chemical shifts This is the 0-7th of these quantities |
cs.cb-0-8 | scalar | the calculated Cb carbon chemical shifts This is the 0-8th of these quantities |
cs.co-0-2 | scalar | the calculated C' carbon chemical shifts This is the 0-2th of these quantities |
cs.co-0-3 | scalar | the calculated C' carbon chemical shifts This is the 0-3th of these quantities |
cs.co-0-4 | scalar | the calculated C' carbon chemical shifts This is the 0-4th of these quantities |
cs.co-0-5 | scalar | the calculated C' carbon chemical shifts This is the 0-5th of these quantities |
cs.co-0-6 | scalar | the calculated C' carbon chemical shifts This is the 0-6th of these quantities |
cs.co-0-7 | scalar | the calculated C' carbon chemical shifts This is the 0-7th of these quantities |
cs.co-0-8 | scalar | the calculated C' carbon chemical shifts This is the 0-8th of these quantities |
cs.ha-0-3 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-3th of these quantities |
cs.ha-0-4 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-4th of these quantities |
cs.ha-0-5 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-5th of these quantities |
cs.ha-0-6 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-6th of these quantities |
cs.ha-0-7 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-7th of these quantities |
cs.ha-0-8 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-8th of these quantities |
cs.hn-0-2 | scalar | the calculated H hydrogen chemical shifts This is the 0-2th of these quantities |
cs.hn-0-3 | scalar | the calculated H hydrogen chemical shifts This is the 0-3th of these quantities |
cs.hn-0-4 | scalar | the calculated H hydrogen chemical shifts This is the 0-4th of these quantities |
cs.hn-0-5 | scalar | the calculated H hydrogen chemical shifts This is the 0-5th of these quantities |
cs.hn-0-6 | scalar | the calculated H hydrogen chemical shifts This is the 0-6th of these quantities |
cs.hn-0-7 | scalar | the calculated H hydrogen chemical shifts This is the 0-7th of these quantities |
cs.hn-0-8 | scalar | the calculated H hydrogen chemical shifts This is the 0-8th of these quantities |
cs.nh-0-2 | scalar | the calculated N nitrogen chemical shifts This is the 0-2th of these quantities |
cs.nh-0-3 | scalar | the calculated N nitrogen chemical shifts This is the 0-3th of these quantities |
cs.nh-0-4 | scalar | the calculated N nitrogen chemical shifts This is the 0-4th of these quantities |
cs.nh-0-5 | scalar | the calculated N nitrogen chemical shifts This is the 0-5th of these quantities |
cs.nh-0-6 | scalar | the calculated N nitrogen chemical shifts This is the 0-6th of these quantities |
cs.nh-0-7 | scalar | the calculated N nitrogen chemical shifts This is the 0-7th of these quantities |
cs.nh-0-8 | scalar | the calculated N nitrogen chemical shifts This is the 0-8th of these quantities |
cs.score | scalar | the Metainference score |
cs.biasDer | scalar | derivatives with respect to the bias |
cs.weight | scalar | weights of the weighted average |
cs.neff | scalar | effective number of replicas |
cs.acceptSigma | scalar | MC acceptance for sigma values |
cs.sigmaMean-0 | scalar | uncertainty in the mean estimate This is the 0th of these quantities |
cs.sigma-0 | scalar | uncertainty parameter This is the 0th of these quantities |
cs.sigmaMean-1 | scalar | uncertainty in the mean estimate This is the 1th of these quantities |
cs.sigma-1 | scalar | uncertainty parameter This is the 1th of these quantities |
cs.sigmaMean-2 | scalar | uncertainty in the mean estimate This is the 2th of these quantities |
cs.sigma-2 | scalar | uncertainty parameter This is the 2th of these quantities |
cs.sigmaMean-3 | scalar | uncertainty in the mean estimate This is the 3th of these quantities |
cs.sigma-3 | scalar | uncertainty parameter This is the 3th of these quantities |
cs.sigmaMean-4 | scalar | uncertainty in the mean estimate This is the 4th of these quantities |
cs.sigma-4 | scalar | uncertainty parameter This is the 4th of these quantities |
cs.sigmaMean-5 | scalar | uncertainty in the mean estimate This is the 5th of these quantities |
cs.sigma-5 | scalar | uncertainty parameter This is the 5th of these quantities |
cs.sigmaMean-6 | scalar | uncertainty in the mean estimate This is the 6th of these quantities |
cs.sigma-6 | scalar | uncertainty parameter This is the 6th of these quantities |
cs.sigmaMean-7 | scalar | uncertainty in the mean estimate This is the 7th of these quantities |
cs.sigma-7 | scalar | uncertainty parameter This is the 7th of these quantities |
cs.sigmaMean-8 | scalar | uncertainty in the mean estimate This is the 8th of these quantities |
cs.sigma-8 | scalar | uncertainty parameter This is the 8th of these quantities |
cs.sigmaMean-9 | scalar | uncertainty in the mean estimate This is the 9th of these quantities |
cs.sigma-9 | scalar | uncertainty parameter This is the 9th of these quantities |
cs.sigmaMean-10 | scalar | uncertainty in the mean estimate This is the 10th of these quantities |
cs.sigma-10 | scalar | uncertainty parameter This is the 10th of these quantities |
cs.sigmaMean-11 | scalar | uncertainty in the mean estimate This is the 11th of these quantities |
cs.sigma-11 | scalar | uncertainty parameter This is the 11th of these quantities |
cs.sigmaMean-12 | scalar | uncertainty in the mean estimate This is the 12th of these quantities |
cs.sigma-12 | scalar | uncertainty parameter This is the 12th of these quantities |
cs.sigmaMean-13 | scalar | uncertainty in the mean estimate This is the 13th of these quantities |
cs.sigma-13 | scalar | uncertainty parameter This is the 13th of these quantities |
cs.sigmaMean-14 | scalar | uncertainty in the mean estimate This is the 14th of these quantities |
cs.sigma-14 | scalar | uncertainty parameter This is the 14th of these quantities |
cs.sigmaMean-15 | scalar | uncertainty in the mean estimate This is the 15th of these quantities |
cs.sigma-15 | scalar | uncertainty parameter This is the 15th of these quantities |
cs.sigmaMean-16 | scalar | uncertainty in the mean estimate This is the 16th of these quantities |
cs.sigma-16 | scalar | uncertainty parameter This is the 16th of these quantities |
cs.sigmaMean-17 | scalar | uncertainty in the mean estimate This is the 17th of these quantities |
cs.sigma-17 | scalar | uncertainty parameter This is the 17th of these quantities |
cs.sigmaMean-18 | scalar | uncertainty in the mean estimate This is the 18th of these quantities |
cs.sigma-18 | scalar | uncertainty parameter This is the 18th of these quantities |
cs.sigmaMean-19 | scalar | uncertainty in the mean estimate This is the 19th of these quantities |
cs.sigma-19 | scalar | uncertainty parameter This is the 19th of these quantities |
cs.sigmaMean-20 | scalar | uncertainty in the mean estimate This is the 20th of these quantities |
cs.sigma-20 | scalar | uncertainty parameter This is the 20th of these quantities |
cs.sigmaMean-21 | scalar | uncertainty in the mean estimate This is the 21th of these quantities |
cs.sigma-21 | scalar | uncertainty parameter This is the 21th of these quantities |
cs.sigmaMean-22 | scalar | uncertainty in the mean estimate This is the 22th of these quantities |
cs.sigma-22 | scalar | uncertainty parameter This is the 22th of these quantities |
cs.sigmaMean-23 | scalar | uncertainty in the mean estimate This is the 23th of these quantities |
cs.sigma-23 | scalar | uncertainty parameter This is the 23th of these quantities |
cs.sigmaMean-24 | scalar | uncertainty in the mean estimate This is the 24th of these quantities |
cs.sigma-24 | scalar | uncertainty parameter This is the 24th of these quantities |
cs.sigmaMean-25 | scalar | uncertainty in the mean estimate This is the 25th of these quantities |
cs.sigma-25 | scalar | uncertainty parameter This is the 25th of these quantities |
cs.sigmaMean-26 | scalar | uncertainty in the mean estimate This is the 26th of these quantities |
cs.sigma-26 | scalar | uncertainty parameter This is the 26th of these quantities |
cs.sigmaMean-27 | scalar | uncertainty in the mean estimate This is the 27th of these quantities |
cs.sigma-27 | scalar | uncertainty parameter This is the 27th of these quantities |
cs.sigmaMean-28 | scalar | uncertainty in the mean estimate This is the 28th of these quantities |
cs.sigma-28 | scalar | uncertainty parameter This is the 28th of these quantities |
cs.sigmaMean-29 | scalar | uncertainty in the mean estimate This is the 29th of these quantities |
cs.sigma-29 | scalar | uncertainty parameter This is the 29th of these quantities |
cs.sigmaMean-30 | scalar | uncertainty in the mean estimate This is the 30th of these quantities |
cs.sigma-30 | scalar | uncertainty parameter This is the 30th of these quantities |
cs.sigmaMean-31 | scalar | uncertainty in the mean estimate This is the 31th of these quantities |
cs.sigma-31 | scalar | uncertainty parameter This is the 31th of these quantities |
cs.sigmaMean-32 | scalar | uncertainty in the mean estimate This is the 32th of these quantities |
cs.sigma-32 | scalar | uncertainty parameter This is the 32th of these quantities |
cs.sigmaMean-33 | scalar | uncertainty in the mean estimate This is the 33th of these quantities |
cs.sigma-33 | scalar | uncertainty parameter This is the 33th of these quantities |
cs.sigmaMean-34 | scalar | uncertainty in the mean estimate This is the 34th of these quantities |
cs.sigma-34 | scalar | uncertainty parameter This is the 34th of these quantities |
cs.sigmaMean-35 | scalar | uncertainty in the mean estimate This is the 35th of these quantities |
cs.sigma-35 | scalar | uncertainty parameter This is the 35th of these quantities |
cs.sigmaMean-36 | scalar | uncertainty in the mean estimate This is the 36th of these quantities |
cs.sigma-36 | scalar | uncertainty parameter This is the 36th of these quantities |
cs.sigmaMean-37 | scalar | uncertainty in the mean estimate This is the 37th of these quantities |
cs.sigma-37 | scalar | uncertainty parameter This is the 37th of these quantities |
cs.sigmaMean-38 | scalar | uncertainty in the mean estimate This is the 38th of these quantities |
cs.sigma-38 | scalar | uncertainty parameter This is the 38th of these quantities |
cs.sigmaMean-39 | scalar | uncertainty in the mean estimate This is the 39th of these quantities |
cs.sigma-39 | scalar | uncertainty parameter This is the 39th of these quantities |
cs.expca-0-2 | scalar | the experimental Ca carbon chemical shifts This is the 0-2th of these quantities |
cs.expca-0-3 | scalar | the experimental Ca carbon chemical shifts This is the 0-3th of these quantities |
cs.expca-0-4 | scalar | the experimental Ca carbon chemical shifts This is the 0-4th of these quantities |
cs.expca-0-5 | scalar | the experimental Ca carbon chemical shifts This is the 0-5th of these quantities |
cs.expca-0-6 | scalar | the experimental Ca carbon chemical shifts This is the 0-6th of these quantities |
cs.expca-0-7 | scalar | the experimental Ca carbon chemical shifts This is the 0-7th of these quantities |
cs.expca-0-8 | scalar | the experimental Ca carbon chemical shifts This is the 0-8th of these quantities |
cs.expcb-0-3 | scalar | the experimental Cb carbon chemical shifts This is the 0-3th of these quantities |
cs.expcb-0-4 | scalar | the experimental Cb carbon chemical shifts This is the 0-4th of these quantities |
cs.expcb-0-5 | scalar | the experimental Cb carbon chemical shifts This is the 0-5th of these quantities |
cs.expcb-0-6 | scalar | the experimental Cb carbon chemical shifts This is the 0-6th of these quantities |
cs.expcb-0-7 | scalar | the experimental Cb carbon chemical shifts This is the 0-7th of these quantities |
cs.expcb-0-8 | scalar | the experimental Cb carbon chemical shifts This is the 0-8th of these quantities |
cs.expco-0-2 | scalar | the experimental C' carbon chemical shifts This is the 0-2th of these quantities |
cs.expco-0-3 | scalar | the experimental C' carbon chemical shifts This is the 0-3th of these quantities |
cs.expco-0-4 | scalar | the experimental C' carbon chemical shifts This is the 0-4th of these quantities |
cs.expco-0-5 | scalar | the experimental C' carbon chemical shifts This is the 0-5th of these quantities |
cs.expco-0-6 | scalar | the experimental C' carbon chemical shifts This is the 0-6th of these quantities |
cs.expco-0-7 | scalar | the experimental C' carbon chemical shifts This is the 0-7th of these quantities |
cs.expco-0-8 | scalar | the experimental C' carbon chemical shifts This is the 0-8th of these quantities |
cs.expha-0-3 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-3th of these quantities |
cs.expha-0-4 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-4th of these quantities |
cs.expha-0-5 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-5th of these quantities |
cs.expha-0-6 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-6th of these quantities |
cs.expha-0-7 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-7th of these quantities |
cs.expha-0-8 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-8th of these quantities |
cs.exphn-0-2 | scalar | the experimental H hydrogen chemical shifts This is the 0-2th of these quantities |
cs.exphn-0-3 | scalar | the experimental H hydrogen chemical shifts This is the 0-3th of these quantities |
cs.exphn-0-4 | scalar | the experimental H hydrogen chemical shifts This is the 0-4th of these quantities |
cs.exphn-0-5 | scalar | the experimental H hydrogen chemical shifts This is the 0-5th of these quantities |
cs.exphn-0-6 | scalar | the experimental H hydrogen chemical shifts This is the 0-6th of these quantities |
cs.exphn-0-7 | scalar | the experimental H hydrogen chemical shifts This is the 0-7th of these quantities |
cs.exphn-0-8 | scalar | the experimental H hydrogen chemical shifts This is the 0-8th of these quantities |
cs.expnh-0-2 | scalar | the experimental N nitrogen chemical shifts This is the 0-2th of these quantities |
cs.expnh-0-3 | scalar | the experimental N nitrogen chemical shifts This is the 0-3th of these quantities |
cs.expnh-0-4 | scalar | the experimental N nitrogen chemical shifts This is the 0-4th of these quantities |
cs.expnh-0-5 | scalar | the experimental N nitrogen chemical shifts This is the 0-5th of these quantities |
cs.expnh-0-6 | scalar | the experimental N nitrogen chemical shifts This is the 0-6th of these quantities |
cs.expnh-0-7 | scalar | the experimental N nitrogen chemical shifts This is the 0-7th of these quantities |
cs.expnh-0-8 | scalar | the experimental N nitrogen chemical shifts This is the 0-8th of these quantities |
: CS2BACKBONECalculates the backbone chemical shifts for a protein. This action has hidden defaults. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSThe atoms to be included in the calculation, e=1-111 DATADIR The folder with the experimental chemical shifts=data TEMPLATE A PDB file of the protein system=template.pdb DOSCORE activate metainference ARGthe labels of the values from which the function is calculated=pb.bias NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MOUTLIERS REWEIGHT simple REWEIGHT using the ARG as energy OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=200 SIGMA0 initial value of the uncertainty parameter=4.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=5.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
cs: CS2BACKBONECalculates the backbone chemical shifts for a protein. This action uses the defaults shown here. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSThe atoms to be included in the calculation, e=1-111 DATADIR The folder with the experimental chemical shifts=data TEMPLATE A PDB file of the protein system=template.pdb DOSCORE activate metainference ARGthe labels of the values from which the function is calculated=pb.bias NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MOUTLIERS REWEIGHT simple REWEIGHT using the ARG as energy OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=200 SIGMA0 initial value of the uncertainty parameter=4.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0001 SIGMA_MAX maximum value of the uncertainty parameter=5.0 DSIGMAmaximum MC move of the uncertainty parameter=0.1 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 NEIGH_FREQ Period in step for neighbor list update=20
mcsThe BIASVALUE action with label mcs calculates the following quantities: Quantity | Type | Description |
mcs.bias | scalar | the instantaneous value of the bias potential |
mcs.cs.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 cs.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=cs.score
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=10000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nh.score,nh.acceptSigma,nh.weight,nh.scale,(nh\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BAYES.RDC.NH
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=caha.score,caha.acceptSigma,caha.weight,caha.scale,(caha\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BAYES.RDC.CAHA
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=byj.* STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BAYES.J
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cs.score,cs.acceptSigma,cs.weight,(cs\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BAYES.CS
ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ...
ARGthe labels of the values from which the function is calculated=(nh\.rdc-.*),(caha\.rdc-.*),pb.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
LABELa label for the action so that its output can be referenced in the input to other actions=ensThe ENSEMBLE action with label ens calculates the following quantities: Quantity | Type | Description |
ens.nh.rdc-0 | scalar | the average for argument nh.rdc-0 |
ens.nh.rdc-1 | scalar | the average for argument nh.rdc-1 |
ens.nh.rdc-2 | scalar | the average for argument nh.rdc-2 |
ens.nh.rdc-3 | scalar | the average for argument nh.rdc-3 |
ens.nh.rdc-4 | scalar | the average for argument nh.rdc-4 |
ens.nh.rdc-5 | scalar | the average for argument nh.rdc-5 |
ens.nh.rdc-6 | scalar | the average for argument nh.rdc-6 |
ens.nh.rdc-7 | scalar | the average for argument nh.rdc-7 |
ens.caha.rdc-0 | scalar | the average for argument caha.rdc-0 |
ens.caha.rdc-1 | scalar | the average for argument caha.rdc-1 |
ens.caha.rdc-2 | scalar | the average for argument caha.rdc-2 |
ens.caha.rdc-3 | scalar | the average for argument caha.rdc-3 |
ens.caha.rdc-4 | scalar | the average for argument caha.rdc-4 |
ens.caha.rdc-5 | scalar | the average for argument caha.rdc-5 |
ens.caha.rdc-6 | scalar | the average for argument caha.rdc-6 |
... ENSEMBLE
STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ...
ARGthe labels of the values from which the function is calculated=(ens\.nh\.rdc-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(nh\.exp-.*)
LABELa label for the action so that its output can be referenced in the input to other actions=nhstThe STATS action with label nhst calculates the following quantities: Quantity | Type | Description |
nhst.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
nhst.corr | scalar | the correlation between arguments and parameters |
nhst.slope | scalar | the slope of a linear fit between arguments and parameters |
nhst.intercept | scalar | the intercept of a linear fit between arguments and parameters |
... STATS
STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ...
ARGthe labels of the values from which the function is calculated=(ens\.caha\.rdc-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(caha\.exp-.*)
LABELa label for the action so that its output can be referenced in the input to other actions=cahastThe STATS action with label cahast calculates the following quantities: Quantity | Type | Description |
cahast.sqdevsum | scalar | the sum of the squared deviations between arguments and parameters |
cahast.corr | scalar | the correlation between arguments and parameters |
cahast.slope | scalar | the slope of a linear fit between arguments and parameters |
cahast.intercept | scalar | the intercept of a linear fit between arguments and parameters |
... STATS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nhst.*,cahast.* FILEthe name of the file on which to output these quantities=STATS STRIDE the frequency with which the quantities of interest should be output=2000
ENDPLUMEDTerminate plumed input. More details