**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

#SETTINGS NREPLICAS=2 # this is optional and tell to VIM that this is a PLUMED file# vim: ft=plumed# see comments just below this input fileEnables 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 detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=template.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-111the atoms that make up a molecule that you wish to align

# CVs, Psi9, Phi1 are not definedpsi1:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi2:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi3:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi4:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi5:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi6:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi7:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi8:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi2:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi3:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi4:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi5:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi6:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi7:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi8:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi9:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distances

# Bulky Trp residue dihedraldihtrp_cacb:TORSIONCalculate a torsional angle. More detailsATOMS=67,47,49,52the four atoms involved in the torsional angledihtrp_cbcg:TORSIONCalculate a torsional angle. More detailsATOMS=47,49,52,53the four atoms involved in the torsional anglegyr:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=the group of atoms that you are calculating the Gyration Tensor for@CA-1,the CA atom in residue 1. Click here for more information.@CA-2,the CA atom in residue 2. Click here for more information.@CA-3,the CA atom in residue 3. Click here for more information.@CA-4,the CA atom in residue 4. Click here for more information.@CA-5,the CA atom in residue 5. Click here for more information.@CA-6,the CA atom in residue 6. Click here for more information.@CA-7,the CA atom in residue 7. Click here for more information.@CA-8,the CA atom in residue 8. Click here for more information.@CA-9the CA atom in residue 9. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distances

# PBMetaDPBMETAD...Used to performed Parallel Bias metadynamics. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspbARG=the input for this action is the scalar output from one or more other actionsphi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcgSIGMA=1000the widths of the Gaussian hillsSIGMA_MIN=0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6the upper bounds for the sigmas (in CV units) when using adaptive hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeHEIGHT=0.5the height of the Gaussian hills, one for all biasesPACE=200the frequency for hill addition, one for all biasesBIASFACTOR=34use well tempered metadynamics with this bias factor, one for all biasesGRID_MIN=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pithe lower bounds for the gridGRID_MAX=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pithe upper bounds for the gridGRID_WSTRIDE=50000frequency for dumping the gridWALKERS_MPI... PBMETADSwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR

# output from the collective variablePrint quantities to a file. More detailsFILE=COLVARthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsgyr,phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcgSTRIDE=2000the frequency with which the quantities of interest should be output

# EXPERIMENTAL DATA SECTION

# RDCs (Grzesiek et al.) # xGAAWAASSRDC...Calculates the (Residual) Dipolar Coupling between two atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesGYROM=-72.5388Add the product of the gyromagnetic constants for the bondSCALE=0.001Add the scaling factor to take into account concentration and other effectsATOMS1=18,19the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING1=-5.4Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS2=25,26the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING2=-1.26Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS3=35,36the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING3=-5.22Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS4=45,46the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING4=-0.91Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS5=69,70the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING5=2.33Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS6=79,80the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING6=-2.88Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS7=89,90the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING7=-8.37Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS8=100,101the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING8=-3.78Add an experimental value for each coupling (needed by SVD and useful for STATS)LABEL=a label for the action so that its output can be referenced in the input to other actionsnhDOSCOREactivate metainferenceARG=the input for this action is the scalar output from one or more other actionspb.biasNOISETYPE=MGAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the ARG as energyOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=200Stride for calculation of averaged weights and sigma_meanREGRES_ZERO=200stride for regression with zero offsetSIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.0001minimum value of the uncertainty parameterSIGMA_MAX=5.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterWRITE_STRIDE=10000 ... RDCwrite the status to a file every N steps, this can be used for restart/continuationmnh:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionsnh.score

# ExAAWAASxRDC...Calculates the (Residual) Dipolar Coupling between two atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesGYROM=179.9319Add the product of the gyromagnetic constants for the bondSCALE=0.001Add the scaling factor to take into account concentration and other effectsATOMS1=5,6the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING1=12.95Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS2=27,28the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING2=11.5Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS3=37,38the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING3=21.42Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS4=47,48the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING4=-9.37Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS5=71,72the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING5=10.01Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS6=81,82the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING6=15.01Add an experimental value for each coupling (needed by SVD and useful for STATS)ATOMS7=91,92the couple of atoms involved in each of the bonds for which you wish to calculate the RDCCOUPLING7=15.73Add an experimental value for each coupling (needed by SVD and useful for STATS)LABEL=a label for the action so that its output can be referenced in the input to other actionscahaDOSCOREactivate metainferenceARG=the input for this action is the scalar output from one or more other actionspb.biasNOISETYPE=MGAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the ARG as energyOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=200Stride for calculation of averaged weights and sigma_meanREGRES_ZERO=200stride for regression with zero offsetSIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.0001minimum value of the uncertainty parameterSIGMA_MAX=5.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterWRITE_STRIDE=10000 ... RDCwrite the status to a file every N steps, this can be used for restart/continuationmcaha:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionscaha.score

# xGxAWxASxJCOUPLING...Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More detailsNOPBCignore the periodic boundary conditions when calculating distancesTYPE=HANType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)ATOMS1=the 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.COUPLING1=-0.49Add an experimental value for each couplingATOMS2=the 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.COUPLING2=-0.54Add an experimental value for each couplingATOMS3=the 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.COUPLING3=-0.53Add an experimental value for each couplingATOMS4=the 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.COUPLING4=-0.39Add an experimental value for each couplingATOMS5=the 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.COUPLING5=-0.39Add an experimental value for each couplingLABEL=a label for the action so that its output can be referenced in the input to other actionsjhan... JCOUPLING

# xxAAWAASSJCOUPLING...Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More detailsNOPBCignore the periodic boundary conditions when calculating distancesTYPE=HAHNType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)ATOMS1=the 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.COUPLING1=6.05Add an experimental value for each couplingATOMS2=the 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.COUPLING2=5.95Add an experimental value for each couplingATOMS3=the 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.COUPLING3=6.44Add an experimental value for each couplingATOMS4=the 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.COUPLING4=6.53Add an experimental value for each couplingATOMS5=the 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.COUPLING5=5.93Add an experimental value for each couplingATOMS6=the 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.COUPLING6=6.98Add an experimental value for each couplingATOMS7=the 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.COUPLING7=7.16Add an experimental value for each couplingLABEL=a label for the action so that its output can be referenced in the input to other actionsjhahn... JCOUPLING

# xxxxWxxxxJCOUPLING...Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More detailsNOPBCignore the periodic boundary conditions when calculating distancesTYPE=CCGType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)ATOMS1=the 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.COUPLING1=1.59Add an experimental value for each couplingLABEL=a label for the action so that its output can be referenced in the input to other actionsjccg... JCOUPLING

# xxxxWxxxxCalculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More detailsNOPBCignore the periodic boundary conditions when calculating distancesTYPE=NCGType of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)ATOMS1=the 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.COUPLING1=1.21Add an experimental value for each couplingLABEL=a label for the action so that its output can be referenced in the input to other actionsjncg... JCOUPLINGMETAINFERENCE...Calculates the Metainference energy for a set of experimental data. More detailsARG=(jhan\.j-.*),(jhahn\.j-.*),(jccg\.j.*),(jncg\.j.*),the input for this action is the scalar output from one or more other actionspb.biasPARARG=(jhan\.exp-.*),(jhahn\.exp-.*),(jccg\.exp.*),(jncg\.expreference values for the experimental data, these can be provided as arguments without derivativesNOISETYPE=MGAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energyOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=200Stride for calculation of averaged weights and sigma_meanSIGMA0=2.5initial value of the uncertainty parameterSIGMA_MIN=0.0001minimum value of the uncertainty parameterSIGMA_MAX=5.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterWRITE_STRIDE=10000write the status to a file every N steps, this can be used for restart/continuationLABEL=a label for the action so that its output can be referenced in the input to other actionsbyj... METAINFERENCE # # Chemical shiftscs:CS2BACKBONECalculates the backbone chemical shifts for a protein. This action has hidden defaults. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=1-111The atoms to be included in the calculation, eDATADIR=dataThe folder with the experimental chemical shiftsTEMPLATE=template.pdbA PDB file of the protein systemDOSCOREactivate metainferenceARG=the input for this action is the scalar output from one or more other actionspb.biasNOISETYPE=MOUTLIERSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the ARG as energyOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=200Stride for calculation of averaged weights and sigma_meanSIGMA0=4.0initial value of the uncertainty parameterSIGMA_MIN=0.0001minimum value of the uncertainty parameterSIGMA_MAX=5.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterWRITE_STRIDE=10000write the status to a file every N steps, this can be used for restart/continuationmcs:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionscs.score

# output from METAINFERENCEFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=10000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsnh.score,nh.acceptSigma,nh.weight,nh.scale,(nh\.sigmaSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=BAYES.RDC.NHthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionscaha.score,caha.acceptSigma,caha.weight,caha.scale,(caha\.sigmaSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=BAYES.RDC.CAHAthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsbyjSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=BAYES.Jthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionscs.score,cs.acceptSigma,cs.weight,(cs\.sigmaSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=BAYES.CSthe name of the file on which to output these quantities

# Calculate weighted ensemble averageENSEMBLE...Calculates the replica averaging of a collective variable over multiple replicas. More detailsARG=(nh\.rdc-.*),(caha\.rdc-.*),the input for this action is the scalar output from one or more other actionspb.biasREWEIGHTsimple REWEIGHT using the latest ARG as energyLABEL=a label for the action so that its output can be referenced in the input to other actionsens... ENSEMBLE

# We use the analogous function for all other observablesSTATS...Calculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(ens\.nh\.rdcthe input for this action is the scalar output from one or more other actionsPARARG=(nh\.expthe input for this action is the scalar output from one or more other actions without derivativesLABEL=a label for the action so that its output can be referenced in the input to other actionsnhst... STATSSTATS...Calculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(ens\.caha\.rdcthe input for this action is the scalar output from one or more other actionsPARARG=(caha\.expthe input for this action is the scalar output from one or more other actions without derivativesLABEL=a label for the action so that its output can be referenced in the input to other actionscahast... STATSPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsnhst.*,cahastFILE=STATSthe name of the file on which to output these quantitiesSTRIDE=2000the frequency with which the quantities of interest should be outputENDPLUMEDTerminate plumed input. More details