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 align
s1: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.NOPBCs2:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs3:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs4:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs5:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs6:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs7:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs8:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs9:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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.NOPBCs10:ignore the periodic boundary conditions when calculating distancesCENTERCalculate 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 More detailsNOPBCignore the periodic boundary conditions when calculating distancesLABEL=backa label for the action so that its output can be referenced in the input to other actionsREFERENCE=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 ... cmap:the coefficient for each of the torsional anglesCONTACTMAP...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=s1,s4the atoms involved in each of the contacts you wish to calculateWEIGHT1=0.02521988A weight value for a given contact, by default is 1ATOMS2=s1,s5the atoms involved in each of the contacts you wish to calculateWEIGHT2=0.20455216A weight value for a given contact, by default is 1ATOMS3=s1,s6the atoms involved in each of the contacts you wish to calculateWEIGHT3=-0.54414755A weight value for a given contact, by default is 1ATOMS4=s1,s7the atoms involved in each of the contacts you wish to calculateWEIGHT4=0.36219968A weight value for a given contact, by default is 1ATOMS5=s1,s8the atoms involved in each of the contacts you wish to calculateWEIGHT5=0.1279484A weight value for a given contact, by default is 1ATOMS6=s1,s9the atoms involved in each of the contacts you wish to calculateWEIGHT6=-0.22453008A weight value for a given contact, by default is 1ATOMS7=s1,s10the atoms involved in each of the contacts you wish to calculateWEIGHT7=0.29550159A weight value for a given contact, by default is 1ATOMS8=s2,s5the atoms involved in each of the contacts you wish to calculateWEIGHT8=-0.03385588A weight value for a given contact, by default is 1ATOMS9=s2,s6the atoms involved in each of the contacts you wish to calculateWEIGHT9=0.09919236A weight value for a given contact, by default is 1ATOMS10=s2,s7the atoms involved in each of the contacts you wish to calculateWEIGHT10=-0.03330457A weight value for a given contact, by default is 1ATOMS11=s2,s8the atoms involved in each of the contacts you wish to calculateWEIGHT11=-0.13847136A weight value for a given contact, by default is 1ATOMS12=s2,s9the atoms involved in each of the contacts you wish to calculateWEIGHT12=0.39094173A weight value for a given contact, by default is 1ATOMS13=s2,s10the atoms involved in each of the contacts you wish to calculateWEIGHT13=-0.1983029A weight value for a given contact, by default is 1ATOMS14=s3,s6the atoms involved in each of the contacts you wish to calculateWEIGHT14=-0.02328201A weight value for a given contact, by default is 1ATOMS15=s3,s7the atoms involved in each of the contacts you wish to calculateWEIGHT15=0.0069981A weight value for a given contact, by default is 1ATOMS16=s3,s8the atoms involved in each of the contacts you wish to calculateWEIGHT16=0.2231250A weight value for a given contact, by default is 1ATOMS17=s3,s9the atoms involved in each of the contacts you wish to calculateWEIGHT17=-0.25618473A weight value for a given contact, by default is 1ATOMS18=s3,s10the atoms involved in each of the contacts you wish to calculateWEIGHT18=0.113674A weight value for a given contact, by default is 1ATOMS19=s4,s7the atoms involved in each of the contacts you wish to calculateWEIGHT19=0.01257499A weight value for a given contact, by default is 1ATOMS20=s4,s8the atoms involved in each of the contacts you wish to calculateWEIGHT20=-0.01498744A weight value for a given contact, by default is 1ATOMS21=s4,s9the atoms involved in each of the contacts you wish to calculateWEIGHT21=-0.11663488A weight value for a given contact, by default is 1ATOMS22=s4,s10the atoms involved in each of the contacts you wish to calculateWEIGHT22=0.084924A weight value for a given contact, by default is 1ATOMS23=s5,s8the atoms involved in each of the contacts you wish to calculateWEIGHT23=-0.005496A weight value for a given contact, by default is 1ATOMS24=s5,s9the atoms involved in each of the contacts you wish to calculateWEIGHT24=0.03150733A weight value for a given contact, by default is 1ATOMS25=s5,s10the atoms involved in each of the contacts you wish to calculateWEIGHT25=-0.03456732A weight value for a given contact, by default is 1ATOMS26=s6,s9the atoms involved in each of the contacts you wish to calculateWEIGHT26=0.00233215A weight value for a given contact, by default is 1ATOMS27=s6,s10the atoms involved in each of the contacts you wish to calculateWEIGHT27=0.01574143A weight value for a given contact, by default is 1ATOMS28=s7,s10the atoms involved in each of the contacts you wish to calculateWEIGHT28=-0.01026257A weight value for a given contact, by default is 1SUM...calculate the sum of all the contacts in the input
rg: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.NOPBChh:ignore the periodic boundary conditions when calculating distancesANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. 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 conditions
mm:PBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=back,cmap,rg,hhthe input for this action is the scalar output from one or more other actionsSIGMA_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=../HILLS.back,../HILLS.cmap,../HILLS.rg,../HILLS.hhfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundGRID_WFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh #GRID_RFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hhdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILESGRID_WSTRIDE=10000 ...frequency for dumping the gridPrint quantities to a file. More detailsARG=back,cmap,rg,hh,mm.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be output