PLUMED-NEST-TEST-SITE

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

Click on the labels of the actions for more information on what each action computes

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=../template.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-166

psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: 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
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: 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
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: 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
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: 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
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: 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
phi4The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi4
scalar
the TORSION involving these atoms: 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
psi4The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi4
scalar
the TORSION involving these atoms: 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
phi5The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi5
scalar
the TORSION involving these atoms: 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
psi5The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi5
scalar
the TORSION involving these atoms: 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
phi6The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi6
scalar
the TORSION involving these atoms: 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
psi6The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi6
scalar
the TORSION involving these atoms: 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
phi7The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7
scalar
the TORSION involving these atoms: 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
psi7The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7
scalar
the TORSION involving these atoms: 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
phi8The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi8
scalar
the TORSION involving these atoms: 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
psi8The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi8
scalar
the TORSION involving these atoms: 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
phi9The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi9
scalar
the TORSION involving these atoms: 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
psi9The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi9
scalar
the TORSION involving these atoms: 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
phi10The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi10
scalar
the TORSION involving these atoms: 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
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: 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=@CA-1the CA atom in residue 1. Click here for more information. ,@CA-2the CA atom in residue 2. Click here for more information. ,@CA-3the CA atom in residue 3. Click here for more information. ,@CA-4the CA atom in residue 4. Click here for more information. ,@CA-5the CA atom in residue 5. Click here for more information. ,@CA-6the CA atom in residue 6. Click here for more information. ,@CA-7the CA atom in residue 7. Click here for more information. ,@CA-8the CA atom in residue 8. Click here for more information. ,@CA-9the CA atom in residue 9. Click here for more information. ,@CA-10the CA atom in residue 10. Click here for more information.  NOPBC ignore the periodic boundary conditions when calculating distances
hhThe ANTIBETARMSD action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf 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 like=1 NOPBC ignore the periodic boundary conditions
hh: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf 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 like=1 NOPBC ignore the periodic boundary conditions  NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# hh: ANTIBETARMSD RESIDUES=all TYPE=DRMSD R_0=0.1 STRANDS_CUTOFF=1 NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
hh_rmsdThe SECONDARY_STRUCTURE_RMSD action with label hh_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_rmsd
vector
a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=1,5,7,22,23,24,26,28,43,44,45,47,49,55,56,57,67,64,69,70,71,73,75,84,85,86,88,90,98,99,100,102,104,105,106,107,109,111,119,120,121,123,125,143,144,145,147,149,164,166 TYPE the manner in which RMSD alignment is performed=DRMSD STRANDS_CUTOFFIf 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 like=1 NOPBC ignore the periodic boundary conditions SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT4this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 1 further SEGMENTn keywords, 
hh_ltThe LESS_THAN action with label hh_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=hh_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12}
hhThe SUM action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=hh_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
mmThe PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: PBMETADUsed to performed Parallel Bias metadynamics. More details ... 
ARGthe labels of the scalars on which the bias will act=psi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hh 
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=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 
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.004,0.02 
SIGMAthe widths of the Gaussian hills=0.015 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM 
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,0.3,0 
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,1.3,3 
HEIGHTthe height of the Gaussian hills, one for all biases=0.5 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=10 PACEthe frequency for hill addition, one for all biases=200 
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR 
FILEfiles 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.hh
GRID_WFILESdump 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.hh
GRID_WSTRIDEfrequency for dumping the grid=10000
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=psi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hh,mm.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1000