Action: LOCALENSEMBLE

Module	function
Description	Usage
Calculates the average over multiple arguments.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Calculates the average over multiple arguments.

If more than one collective variable is given for each argument then they are averaged separately. The average is stored in a component labelled label.cvlabel.

Examples

The following input tells plumed to calculate the chemical shifts for four different proteins in the same simulation box then average them, calculated the sum of the squared deviation with respect to the experimental values and applies a linear restraint.

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=data/template.pdb

The MOLINFO action with label  calculates somethingchaina: 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=1-1640
The GROUP action with label chaina calculates somethingchainb: 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=1641-3280
The GROUP action with label chainb calculates somethingchainc: 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=3281-4920
The GROUP action with label chainc calculates somethingchaind: 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=4921-6560

The GROUP action with label chaind 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=chaina ENTITY1the atoms that make up a molecule that you wish to align=chainb ENTITY2the atoms that make up a molecule that you wish to align=chainc ENTITY3the atoms that make up a molecule that you wish to align=chaind

csa: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=chaina NRES=100 DATA=data/ TEMPLATE A PDB file of the protein system=chaina.pdb NOPBC ignore the periodic boundary conditions when calculating distances
The CS2BACKBONE action with label csa calculates the following quantities:
 Quantity   
 Description  
csa.score
the Metainference score
csa.sigma
uncertainty parameter
csa.sigmaMean
uncertainty in the mean estimate
csa.neff
effective number of replicas
csa.acceptSigma
MC acceptance for sigma values
csa.ha
the calculated Ha hydrogen chemical shifts
csa.hn
the calculated H hydrogen chemical shifts
csa.nh
the calculated N nitrogen chemical shifts
csa.ca
the calculated Ca carbon chemical shifts
csa.cb
the calculated Cb carbon chemical shifts
csa.co
the calculated C' carbon chemical shifts
csa.expha
the experimental Ha hydrogen chemical shifts
csa.exphn
the experimental H hydrogen chemical shifts
csa.expnh
the experimental N nitrogen chemical shifts
csa.expca
the experimental Ca carbon chemical shifts
csa.expcb
the experimental Cb carbon chemical shifts
csa.expco
the experimental C' carbon chemical shifts
csa.value
the backbone chemical shiftscsb: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=chainb NRES=100 DATA=data/ TEMPLATE A PDB file of the protein system=chainb.pdb NOPBC ignore the periodic boundary conditions when calculating distances
The CS2BACKBONE action with label csb calculates the following quantities:
 Quantity   
 Description  
csb.score
the Metainference score
csb.sigma
uncertainty parameter
csb.sigmaMean
uncertainty in the mean estimate
csb.neff
effective number of replicas
csb.acceptSigma
MC acceptance for sigma values
csb.ha
the calculated Ha hydrogen chemical shifts
csb.hn
the calculated H hydrogen chemical shifts
csb.nh
the calculated N nitrogen chemical shifts
csb.ca
the calculated Ca carbon chemical shifts
csb.cb
the calculated Cb carbon chemical shifts
csb.co
the calculated C' carbon chemical shifts
csb.expha
the experimental Ha hydrogen chemical shifts
csb.exphn
the experimental H hydrogen chemical shifts
csb.expnh
the experimental N nitrogen chemical shifts
csb.expca
the experimental Ca carbon chemical shifts
csb.expcb
the experimental Cb carbon chemical shifts
csb.expco
the experimental C' carbon chemical shifts
csb.value
the backbone chemical shiftscsc: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=chainc NRES=100 DATA=data/ TEMPLATE A PDB file of the protein system=chainc.pdb NOPBC ignore the periodic boundary conditions when calculating distances
The CS2BACKBONE action with label csc calculates the following quantities:
 Quantity   
 Description  
csc.score
the Metainference score
csc.sigma
uncertainty parameter
csc.sigmaMean
uncertainty in the mean estimate
csc.neff
effective number of replicas
csc.acceptSigma
MC acceptance for sigma values
csc.ha
the calculated Ha hydrogen chemical shifts
csc.hn
the calculated H hydrogen chemical shifts
csc.nh
the calculated N nitrogen chemical shifts
csc.ca
the calculated Ca carbon chemical shifts
csc.cb
the calculated Cb carbon chemical shifts
csc.co
the calculated C' carbon chemical shifts
csc.expha
the experimental Ha hydrogen chemical shifts
csc.exphn
the experimental H hydrogen chemical shifts
csc.expnh
the experimental N nitrogen chemical shifts
csc.expca
the experimental Ca carbon chemical shifts
csc.expcb
the experimental Cb carbon chemical shifts
csc.expco
the experimental C' carbon chemical shifts
csc.value
the backbone chemical shiftscsd: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=chaind NRES=100 DATA=data/ TEMPLATE A PDB file of the protein system=chaind.pdb NOPBC ignore the periodic boundary conditions when calculating distances

The CS2BACKBONE action with label csd calculates the following quantities:
 Quantity   
 Description  
csd.score
the Metainference score
csd.sigma
uncertainty parameter
csd.sigmaMean
uncertainty in the mean estimate
csd.neff
effective number of replicas
csd.acceptSigma
MC acceptance for sigma values
csd.ha
the calculated Ha hydrogen chemical shifts
csd.hn
the calculated H hydrogen chemical shifts
csd.nh
the calculated N nitrogen chemical shifts
csd.ca
the calculated Ca carbon chemical shifts
csd.cb
the calculated Cb carbon chemical shifts
csd.co
the calculated C' carbon chemical shifts
csd.expha
the experimental Ha hydrogen chemical shifts
csd.exphn
the experimental H hydrogen chemical shifts
csd.expnh
the experimental N nitrogen chemical shifts
csd.expca
the experimental Ca carbon chemical shifts
csd.expcb
the experimental Cb carbon chemical shifts
csd.expco
the experimental C' carbon chemical shifts
csd.value
the backbone chemical shiftsensca: LOCALENSEMBLECalculates the average over multiple arguments. More details NUMthe number of local replicas=4 ARG1the labels of the actions that you want to use=(csa\.ca_.*) ARG2the labels of the actions that you want to use=(csb\.ca_.*) ARG3the labels of the actions that you want to use=(csc\.ca_.*) ARG4the labels of the actions that you want to use=(csd\.ca_.*)
The LOCALENSEMBLE action with label ensca calculates the following quantities:
 Quantity   
 Description  
ensca..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsenscb: LOCALENSEMBLECalculates the average over multiple arguments. More details NUMthe number of local replicas=4 ARG1the labels of the actions that you want to use=(csa\.cb_.*) ARG2the labels of the actions that you want to use=(csb\.cb_.*) ARG3the labels of the actions that you want to use=(csc\.cb_.*) ARG4the labels of the actions that you want to use=(csd\.cb_.*)
The LOCALENSEMBLE action with label enscb calculates the following quantities:
 Quantity   
 Description  
enscb..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsensco: LOCALENSEMBLECalculates the average over multiple arguments. More details NUMthe number of local replicas=4 ARG1the labels of the actions that you want to use=(csa\.co_.*) ARG2the labels of the actions that you want to use=(csb\.co_.*) ARG3the labels of the actions that you want to use=(csc\.co_.*) ARG4the labels of the actions that you want to use=(csd\.co_.*)
The LOCALENSEMBLE action with label ensco calculates the following quantities:
 Quantity   
 Description  
ensco..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsenshn: LOCALENSEMBLECalculates the average over multiple arguments. More details NUMthe number of local replicas=4 ARG1the labels of the actions that you want to use=(csa\.hn_.*) ARG2the labels of the actions that you want to use=(csb\.hn_.*) ARG3the labels of the actions that you want to use=(csc\.hn_.*) ARG4the labels of the actions that you want to use=(csd\.hn_.*)
The LOCALENSEMBLE action with label enshn calculates the following quantities:
 Quantity   
 Description  
enshn..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsensnh: LOCALENSEMBLECalculates the average over multiple arguments. More details NUMthe number of local replicas=4 ARG1the labels of the actions that you want to use=(csa\.nh_.*) ARG2the labels of the actions that you want to use=(csb\.nh_.*) ARG3the labels of the actions that you want to use=(csc\.nh_.*) ARG4the labels of the actions that you want to use=(csd\.nh_.*)

The LOCALENSEMBLE action with label ensnh calculates the following quantities:
 Quantity   
 Description  
ensnh..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsstca: 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=(ensca\.csa\.ca_.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(csa\.expca_.*) SQDEVSUM calculates only SQDEVSUM
The STATS action with label stca calculates the following quantities:
 Quantity   
 Description  
stca.sqdevsum
the sum of the squared deviations between arguments and parameters
stca.corr
the correlation between arguments and parameters
stca.slope
the slope of a linear fit between arguments and parameters
stca.intercept
the intercept of a linear fit between arguments and parametersstcb: 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=(enscb\.csa\.cb_.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(csa\.expcb_.*) SQDEVSUM calculates only SQDEVSUM
The STATS action with label stcb calculates the following quantities:
 Quantity   
 Description  
stcb.sqdevsum
the sum of the squared deviations between arguments and parameters
stcb.corr
the correlation between arguments and parameters
stcb.slope
the slope of a linear fit between arguments and parameters
stcb.intercept
the intercept of a linear fit between arguments and parametersstco: 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=(ensco\.csa\.co_.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(csa\.expco_.*) SQDEVSUM calculates only SQDEVSUM
The STATS action with label stco calculates the following quantities:
 Quantity   
 Description  
stco.sqdevsum
the sum of the squared deviations between arguments and parameters
stco.corr
the correlation between arguments and parameters
stco.slope
the slope of a linear fit between arguments and parameters
stco.intercept
the intercept of a linear fit between arguments and parameterssthn: 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=(enshn\.csa\.hn_.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(csa\.exphn_.*) SQDEVSUM calculates only SQDEVSUM
The STATS action with label sthn calculates the following quantities:
 Quantity   
 Description  
sthn.sqdevsum
the sum of the squared deviations between arguments and parameters
sthn.corr
the correlation between arguments and parameters
sthn.slope
the slope of a linear fit between arguments and parameters
sthn.intercept
the intercept of a linear fit between arguments and parametersstnh: 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=(ensnh\.csa\.nh_.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(csa\.expnh_.*) SQDEVSUM calculates only SQDEVSUM

The STATS action with label stnh calculates the following quantities:
 Quantity   
 Description  
stnh.sqdevsum
the sum of the squared deviations between arguments and parameters
stnh.corr
the correlation between arguments and parameters
stnh.slope
the slope of a linear fit between arguments and parameters
stnh.intercept
the intercept of a linear fit between arguments and parametersres: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=stca.*,stcb.*,stco.*,sthn.*,stnh.* ATthe position of the restraint=0.,0.,0.,0.,0. KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=0.,0.,0.,0.,0 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=16.,16.,12.,24.,0.5
The RESTRAINT action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
res.force2
the instantaneous value of the squared force due to this bias potential

Syntax

The following table describes the keywords and options that can be used with this action