**Project ID:** plumID:21.014

**Source:** PLUMED-NEST_chignolin/Part1_MetaD_PBMetaD/plumed_PB20.dat

**Originally used with PLUMED version:** 2.7

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

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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../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=1-166the atoms that make up a molecule that you wish to alignpsi1: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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 distancesrg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsATOMS=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-9,the CA atom in residue 9. Click here for more information.@CA-10the CA atom in residue 10. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distanceshh:ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More detailsRESIDUES=allthis command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedR_0=0.1The r_0 parameter of the switching functionSTRANDS_CUTOFF=1If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet likeNOPBCignore the periodic boundary conditionsmm:PBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=the input for this action is the scalar output from one or more other actionspsi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hhSIGMA_MAX=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6the upper bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MIN=0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.004,0.02the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA=0.015the widths of the Gaussian hillsADAPTIVE=GEOMuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeGRID_MIN=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.3,0the lower bounds for the gridGRID_MAX=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,1.3,3the upper bounds for the gridHEIGHT=0.5the height of the Gaussian hills, one for all biasesBIASFACTOR=10use well tempered metadynamics with this bias factor, one for all biasesPACE=200the frequency for hill addition, one for all biasesWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRFILE=files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found../HILLS.psi1,../HILLS.phi2,../HILLS.psi2,../HILLS.phi3,../HILLS.psi3,../HILLS.phi4,../HILLS.psi4,../HILLS.phi5,../HILLS.psi5,../HILLS.phi6,../HILLS.psi6,../HILLS.phi7,../HILLS.psi7,../HILLS.phi8,../HILLS.psi8,../HILLS.phi9,../HILLS.psi9,../HILLS.phi10,../HILLS.rg,../HILLS.hhGRID_WFILES=dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES../GRID.psi1,../GRID.phi2,../GRID.psi2,../GRID.phi3,../GRID.psi3,../GRID.phi4,../GRID.psi4,../GRID.phi5,../GRID.psi5,../GRID.phi6,../GRID.psi6,../GRID.phi7,../GRID.psi7,../GRID.phi8,../GRID.psi8,../GRID.phi9,../GRID.psi9,../GRID.phi10,../GRID.rg,../GRID.hh#GRID_RFILES=../GRID.psi1,../GRID.phi2,../GRID.psi2,../GRID.phi3,../GRID.psi3,../GRID.phi4,../GRID.psi4,../GRID.phi5,../GRID.psi5,../GRID.phi6,../GRID.psi6,../GRID.phi7,../GRID.psi7,../GRID.phi8,../GRID.psi8,../GRID.phi9,../GRID.psi9,../GRID.phi10,../GRID.rg,../GRID.hhGRID_WSTRIDE=10000 ...frequency for dumping the gridPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionspsi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hh,mm.biasFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be output