**Project ID:** plumID:21.014

**Source:** PLUMED-NEST_chignolin/Part1_MetaD_PBMetaD/plumed_PB4.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 aligns1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-1the protein/dna/rna backbone atoms in residue 1. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess2:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-2the protein/dna/rna backbone atoms in residue 2. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess3:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-3the protein/dna/rna backbone atoms in residue 3. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess4:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-4the protein/dna/rna backbone atoms in residue 4. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess5:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-5the protein/dna/rna backbone atoms in residue 5. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess6:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-6the protein/dna/rna backbone atoms in residue 6. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess7:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-7the protein/dna/rna backbone atoms in residue 7. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess8:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-8the protein/dna/rna backbone atoms in residue 8. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess9:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-9the protein/dna/rna backbone atoms in residue 9. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancess10:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@back-10the protein/dna/rna backbone atoms in residue 10. Click here for more information.NOPBCignore the periodic boundary conditions when calculating distancesALPHABETA...Calculate the alpha beta CV This action is a shortcut. More detailsNOPBCignore the periodic boundary conditions when calculating distancesLABEL=a label for the action so that its output can be referenced in the input to other actionsbackREFERENCE=0the reference values for each of the torsional anglesATOMS1=the atoms involved for each of the torsions you wish to calculate@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.COEFFICIENT1=-0.01427455the coefficient for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.COEFFICIENT2=-0.03003557the coefficient for each of the torsional anglesATOMS3=the atoms involved for each of the torsions you wish to calculate@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.COEFFICIENT3=-0.23777775the coefficient for each of the torsional anglesATOMS4=the atoms involved for each of the torsions you wish to calculate@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.COEFFICIENT4=0.139227the coefficient for each of the torsional anglesATOMS5=the atoms involved for each of the torsions you wish to calculate@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.COEFFICIENT5=0.26525215the coefficient for each of the torsional anglesATOMS6=the atoms involved for each of the torsions you wish to calculate@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.COEFFICIENT6=-0.18108167the coefficient for each of the torsional anglesATOMS7=the atoms involved for each of the torsions you wish to calculate@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.COEFFICIENT7=0.01530576the coefficient for each of the torsional anglesATOMS8=the atoms involved for each of the torsions you wish to calculate@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.COEFFICIENT8=0.07231603the coefficient for each of the torsional anglesATOMS9=the atoms involved for each of the torsions you wish to calculate@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.COEFFICIENT9=-0.1183752the coefficient for each of the torsional anglesATOMS10=the atoms involved for each of the torsions you wish to calculate@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.COEFFICIENT10=0.00089293the coefficient for each of the torsional anglesATOMS11=the atoms involved for each of the torsions you wish to calculate@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.COEFFICIENT11=-0.23744683the coefficient for each of the torsional anglesATOMS12=the atoms involved for each of the torsions you wish to calculate@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.COEFFICIENT12=0.15661255the coefficient for each of the torsional anglesATOMS13=the atoms involved for each of the torsions you wish to calculate@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.COEFFICIENT13=0.63855605the coefficient for each of the torsional anglesATOMS14=the atoms involved for each of the torsions you wish to calculate@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.COEFFICIENT14=-0.15161411the coefficient for each of the torsional anglesATOMS15=the atoms involved for each of the torsions you wish to calculate@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.COEFFICIENT15=0.50759965the coefficient for each of the torsional anglesATOMS16=the atoms involved for each of the torsions you wish to calculate@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.COEFFICIENT16=-0.04886669the coefficient for each of the torsional anglesATOMS17=the atoms involved for each of the torsions you wish to calculate@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.COEFFICIENT17=0.13599118the coefficient for each of the torsional anglesATOMS18=the atoms involved for each of the torsions you wish to calculate@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.COEFFICIENT18=-0.1007816 ...the coefficient for each of the torsional anglescmap:CONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsNOPBCignore the periodic boundary conditions when calculating distancesSWITCH={RATIONAL R_0=0.6}The switching functions to use for each of the contacts in your mapATOMS1=the atoms involved in each of the contacts you wish to calculates1,s4WEIGHT1=0.02521988A weight value for a given contact, by default is 1ATOMS2=the atoms involved in each of the contacts you wish to calculates1,s5WEIGHT2=0.20455216A weight value for a given contact, by default is 1ATOMS3=the atoms involved in each of the contacts you wish to calculates1,s6WEIGHT3=-0.54414755A weight value for a given contact, by default is 1ATOMS4=the atoms involved in each of the contacts you wish to calculates1,s7WEIGHT4=0.36219968A weight value for a given contact, by default is 1ATOMS5=the atoms involved in each of the contacts you wish to calculates1,s8WEIGHT5=0.1279484A weight value for a given contact, by default is 1ATOMS6=the atoms involved in each of the contacts you wish to calculates1,s9WEIGHT6=-0.22453008A weight value for a given contact, by default is 1ATOMS7=the atoms involved in each of the contacts you wish to calculates1,s10WEIGHT7=0.29550159A weight value for a given contact, by default is 1ATOMS8=the atoms involved in each of the contacts you wish to calculates2,s5WEIGHT8=-0.03385588A weight value for a given contact, by default is 1ATOMS9=the atoms involved in each of the contacts you wish to calculates2,s6WEIGHT9=0.09919236A weight value for a given contact, by default is 1ATOMS10=the atoms involved in each of the contacts you wish to calculates2,s7WEIGHT10=-0.03330457A weight value for a given contact, by default is 1ATOMS11=the atoms involved in each of the contacts you wish to calculates2,s8WEIGHT11=-0.13847136A weight value for a given contact, by default is 1ATOMS12=the atoms involved in each of the contacts you wish to calculates2,s9WEIGHT12=0.39094173A weight value for a given contact, by default is 1ATOMS13=the atoms involved in each of the contacts you wish to calculates2,s10WEIGHT13=-0.1983029A weight value for a given contact, by default is 1ATOMS14=the atoms involved in each of the contacts you wish to calculates3,s6WEIGHT14=-0.02328201A weight value for a given contact, by default is 1ATOMS15=the atoms involved in each of the contacts you wish to calculates3,s7WEIGHT15=0.0069981A weight value for a given contact, by default is 1ATOMS16=the atoms involved in each of the contacts you wish to calculates3,s8WEIGHT16=0.2231250A weight value for a given contact, by default is 1ATOMS17=the atoms involved in each of the contacts you wish to calculates3,s9WEIGHT17=-0.25618473A weight value for a given contact, by default is 1ATOMS18=the atoms involved in each of the contacts you wish to calculates3,s10WEIGHT18=0.113674A weight value for a given contact, by default is 1ATOMS19=the atoms involved in each of the contacts you wish to calculates4,s7WEIGHT19=0.01257499A weight value for a given contact, by default is 1ATOMS20=the atoms involved in each of the contacts you wish to calculates4,s8WEIGHT20=-0.01498744A weight value for a given contact, by default is 1ATOMS21=the atoms involved in each of the contacts you wish to calculates4,s9WEIGHT21=-0.11663488A weight value for a given contact, by default is 1ATOMS22=the atoms involved in each of the contacts you wish to calculates4,s10WEIGHT22=0.084924A weight value for a given contact, by default is 1ATOMS23=the atoms involved in each of the contacts you wish to calculates5,s8WEIGHT23=-0.005496A weight value for a given contact, by default is 1ATOMS24=the atoms involved in each of the contacts you wish to calculates5,s9WEIGHT24=0.03150733A weight value for a given contact, by default is 1ATOMS25=the atoms involved in each of the contacts you wish to calculates5,s10WEIGHT25=-0.03456732A weight value for a given contact, by default is 1ATOMS26=the atoms involved in each of the contacts you wish to calculates6,s9WEIGHT26=0.00233215A weight value for a given contact, by default is 1ATOMS27=the atoms involved in each of the contacts you wish to calculates6,s10WEIGHT27=0.01574143A weight value for a given contact, by default is 1ATOMS28=the atoms involved in each of the contacts you wish to calculates7,s10WEIGHT28=-0.01026257A weight value for a given contact, by default is 1SUM...calculate the sum of all the contacts in the inputrg: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@N-1,the N atom in residue 1. Click here for more information.@CA-1,the CA atom in residue 1. Click here for more information.@C-1,the C atom in residue 1. Click here for more information.@N-2,the N atom in residue 2. Click here for more information.@CA-2,the CA atom in residue 2. Click here for more information.@C-2,the C atom in residue 2. Click here for more information.@N-3,the N atom in residue 3. Click here for more information.@CA-3,the CA atom in residue 3. Click here for more information.@C-3,the C atom in residue 3. Click here for more information.@N-4,the N atom in residue 4. Click here for more information.@CA-4,the CA atom in residue 4. Click here for more information.@C-4,the C atom in residue 4. Click here for more information.@N-5,the N atom in residue 5. Click here for more information.@CA-5,the CA atom in residue 5. Click here for more information.@C-5,the C atom in residue 5. Click here for more information.@N-6,the N atom in residue 6. Click here for more information.@CA-6,the CA atom in residue 6. Click here for more information.@C-6,the C atom in residue 6. Click here for more information.@N-7,the N atom in residue 7. Click here for more information.@CA-7,the CA atom in residue 7. Click here for more information.@C-7,the C atom in residue 7. Click here for more information.@N-8,the N atom in residue 8. Click here for more information.@CA-8,the CA atom in residue 8. Click here for more information.@C-8,the C atom in residue 8. Click here for more information.@N-9,the N atom in residue 9. Click here for more information.@CA-9,the CA atom in residue 9. Click here for more information.@C-9,the C atom in residue 9. Click here for more information.@N-10,the N atom in residue 10. Click here for more information.@CA-10,the CA atom in residue 10. Click here for more information.@C-10the C 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 actionsback,cmap,rg,hhSIGMA_MAX=0.2,0.2,0.2,0.2the upper bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MIN=0.01,0.001,0.004,0.02the 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=-4,-2,0.3,0the lower bounds for the gridGRID_MAX=4,2,1.4,3the 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.back,../HILLS.cmap,../HILLS.rg,../HILLS.hhGRID_WFILES=dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh#GRID_RFILES=../GRID.back,../GRID.cmap,../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 actionsback,cmap,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