**Project ID:** plumID:22.035

**Source:** wt_helix.dat

**Originally used with PLUMED version:** 2.6.1

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

# RESTART # Define CVs. Phi, psiMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=wt_helix_H.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=1-333the atoms that make up a molecule that you wish to align

# Dihedral anglespsi1: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 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 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 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 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 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 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 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 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 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 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 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 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 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 distancespsi9:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.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 distancespsi10:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi10:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi11:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi11:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi12:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi12:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi13:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi13:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi14:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi14:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi15:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi15:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi16:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi16:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi17:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi17:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi18:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi18:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi19:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi19:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi20:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi20:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancespsi21:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi21:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesphi22:TORSIONCalculate a torsional angle. More detailsATOMS=the 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.NOPBCignore the periodic boundary conditions when calculating distancesPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=the input for this action is the scalar output from one or more other actionspsi1,psi2,phi2,psi3,phi3,psi4,phi4,psi5,phi5,psi6,phi6,psi7,phi7,psi8,phi8,psi9,phi9,psi10,phi10,psi11,phi11,psi12,phi12,psi13,phi13,psi14,phi14,psi15,phi15,psi16,phi16,psi17,phi17,psi18,phi18,psi19,phi19,psi20,phi20,psi21,phi21,phi22ADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA=1000the widths of the Gaussian hillsPACE=200the frequency for hill addition, one for all biasesHEIGHT=0.3the height of the Gaussian hills, one for all biasesBIASFACTOR=32use well tempered metadynamics with this bias factor, one for all biasesLABEL=a label for the action so that its output can be referenced in the input to other actionspbSIGMA_MIN=0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6the upper bounds for the sigmas (in CV units) when using adaptive hillsINTERVAL_MIN=-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,-pione dimensional lower limits, outside the limits the system will not feel the biasing forceINTERVAL_MAX=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,pione dimensional upper limits, outside the limits the system will not feel the biasing forceGRID_MIN=-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,-pithe lower bounds for the gridGRID_MAX=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,pithe upper bounds for the gridGRID_WSTRIDE=900000000 ... PBMETADfrequency for dumping the grid