Project ID: plumID:23.008
Source: plumed_analysis.dat
Originally used with PLUMED version: 2.5.0
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
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#RESTART
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=hst5.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=1-417 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 phi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-20the four atoms that are required to calculate the phi dihedral for residue 20. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-21the four atoms that are required to calculate the phi dihedral for residue 21. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-22the four atoms that are required to calculate the phi dihedral for residue 22. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-23the four atoms that are required to calculate the phi dihedral for residue 23. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances phi24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-24the four atoms that are required to calculate the phi dihedral for residue 24. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
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 psi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi15: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances psi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. NOPBC ignore the periodic boundary conditions when calculating distances
ca: 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 NDX_FILEthe name of index file (gromacs syntax)=hst5.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=C-alpha rg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-417 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=pbmetad WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR ARGthe labels of the scalars on which the bias will act=phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,phi11,phi12,phi13,phi14,phi15,phi16,phi17,phi18,phi19,phi20,phi21,phi22,phi23,phi24,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,psi12,psi13,psi14,psi15,psi16,psi17,psi18,psi19,psi20,psi21,psi22,psi23,rg PACEthe frequency for hill addition, one for all biases=90000000 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=24 HEIGHTthe height of the Gaussian hills, one for all biases=0.3 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMAthe widths of the Gaussian hills=1000 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.001 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.4 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,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.4 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,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,2.8 INTERVAL_MINone dimensional lower limits, outside the limits the system will not feel the biasing force=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.60 INTERVAL_MAXone dimensional upper limits, outside the limits the system will not feel the biasing force=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,2.50 #GRID_RFILES=GRID.phi2,GRID.phi3,GRID.phi4,GRID.phi5,GRID.phi6,GRID.phi7,GRID.phi8,GRID.phi9,GRID.phi10,GRID.phi11,GRID.phi12,GRID.phi13,GRID.phi14,GRID.phi15,GRID.phi16,GRID.phi17,GRID.phi18,GRID.phi19,GRID.phi20,GRID.phi21,GRID.phi22,GRID.phi23,GRID.phi24,GRID.psi1,GRID.psi2,GRID.psi3,GRID.psi4,GRID.psi5,GRID.psi6,GRID.psi7,GRID.psi8,GRID.psi9,GRID.psi10,GRID.psi11,GRID.psi12,GRID.psi13,GRID.psi14,GRID.psi15,GRID.psi16,GRID.psi17,GRID.psi18,GRID.psi19,GRID.psi20,GRID.psi21,GRID.psi22,GRID.psi23,GRID.rg TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 ... PBMETAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=CV_PHI ARGthe labels of the values that you would like to print to the file=phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,phi11,phi12,phi13,phi14,phi15,phi16,phi17,phi18,phi19,phi20,phi21,phi22,phi23,phi24 PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=CV_PSI ARGthe labels of the values that you would like to print to the file=psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,psi12,psi13,psi14,psi15,psi16,psi17,psi18,psi19,psi20,psi21,psi22,psi23 PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=RG_BIAS ARGthe labels of the values that you would like to print to the file=rg,pbmetad.bias