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
tested onv2.10
tested onmaster
#SETTINGS NREPLICAS=2
# this is optional and tell to VIM that this is a PLUMED file
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# see comments just below this input file
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
WHOLEMOLECULESThis 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

# CVs, Psi9, Phi1 are not defined
psi1: 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
psi2: 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
psi3: 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
psi4: 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
psi5: 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
psi6: 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
psi7: 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
psi8: 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

phi2: 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 phi3: 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 phi4: 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 phi5: 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 phi6: 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 phi7: 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 phi8: 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 phi9: 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
# Bulky Trp residue dihedral dihtrp_cacb: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=67,47,49,52 dihtrp_cbcg: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=47,49,52,53 gyr: 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
# PBMetaD 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=pb 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
# output from the collective variable 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 # EXPERIMENTAL DATA SECTION
# RDCs (Grzesiek et al.) # xGAAWAASS 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=nh 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
mnh: 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 # ExAAWAASx 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=caha 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
mcaha: 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 # xGxAWxASx 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=jhan ... JCOUPLING
# xxAAWAASS 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=jhahn ... JCOUPLING
# xxxxWxxxx 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=jccg ... JCOUPLING
# xxxxWxxxx 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=jncg ... 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=byj ... METAINFERENCE # # Chemical shifts cs: 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 mcs: 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 # output from METAINFERENCE 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 # Calculate weighted ensemble average 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=ens ... ENSEMBLE
# We use the analogous function for all other observables 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=nhst ... 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=cahast ... 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