PLUMED-NEST

Project ID: plumID:22.007
Source: metad_wte/plumed.dat
Originally used with PLUMED version: 2.5.3
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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=reference.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
#chain A and B atoms
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-1988 
ENTITY1
the atoms that make up a molecule that you wish to align
=1989-2366 # For fixing PBC problems

#CZ of ARG 76-A and CD of GLU 240-B
d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1178,2244

#to monitor only
#helical content of the region - psi angle
The DISTANCE action with label d1 calculates a scalar quantity
ALPHABETA
Calculate the alpha beta CV More details
 ...
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@psi-239
the four atoms that are required to calculate the psi dihedral for residue 239. Click here for more information. 
 
REFERENCE1
the reference values for each of the torsional angles
=-0.79
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@psi-240
the four atoms that are required to calculate the psi dihedral for residue 240. Click here for more information. 
 
REFERENCE2
the reference values for each of the torsional angles
=-0.79
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@psi-241
the four atoms that are required to calculate the psi dihedral for residue 241. Click here for more information. 
 
REFERENCE3
the reference values for each of the torsional angles
=-0.79
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@psi-242
the four atoms that are required to calculate the psi dihedral for residue 242. Click here for more information. 
 
REFERENCE4
the reference values for each of the torsional angles
=-0.79
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@psi-243
the four atoms that are required to calculate the psi dihedral for residue 243. Click here for more information. 
 
REFERENCE5
the reference values for each of the torsional angles
=-0.79
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@psi-244
the four atoms that are required to calculate the psi dihedral for residue 244. Click here for more information. 
 
REFERENCE6
the reference values for each of the torsional angles
=-0.79
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@psi-245
the four atoms that are required to calculate the psi dihedral for residue 245. Click here for more information. 
 
REFERENCE7
the reference values for each of the torsional angles
=-0.79
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@psi-246
the four atoms that are required to calculate the psi dihedral for residue 246. Click here for more information. 
 
REFERENCE8
the reference values for each of the torsional angles
=-0.79
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab-psi
... ALPHABETA
#helical content of the region phi angle
ALPHABETA
Calculate the alpha beta CV More details
 ...
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@phi-239
the four atoms that are required to calculate the phi dihedral for residue 239. Click here for more information. 
 
REFERENCE1
the reference values for each of the torsional angles
=-1.05
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@phi-240
the four atoms that are required to calculate the phi dihedral for residue 240. Click here for more information. 
 
REFERENCE2
the reference values for each of the torsional angles
=-1.05
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@phi-241
the four atoms that are required to calculate the phi dihedral for residue 241. Click here for more information. 
 
REFERENCE3
the reference values for each of the torsional angles
=-1.05
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@phi-242
the four atoms that are required to calculate the phi dihedral for residue 242. Click here for more information. 
 
REFERENCE4
the reference values for each of the torsional angles
=-1.05
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@phi-243
the four atoms that are required to calculate the phi dihedral for residue 243. Click here for more information. 
 
REFERENCE5
the reference values for each of the torsional angles
=-1.05
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@phi-244
the four atoms that are required to calculate the phi dihedral for residue 244. Click here for more information. 
 
REFERENCE6
the reference values for each of the torsional angles
=-1.05
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@phi-245
the four atoms that are required to calculate the phi dihedral for residue 245. Click here for more information. 
 
REFERENCE7
the reference values for each of the torsional angles
=-1.05
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@phi-246
the four atoms that are required to calculate the phi dihedral for residue 246. Click here for more information. 
 
REFERENCE8
the reference values for each of the torsional angles
=-1.05
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab-phi
... ALPHABETA

#alphaRMSD
alpha_rmsd: 
ALPHARMSD
Probe the alpha helical content of a protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=239-246 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.08 
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function
=8 
MM
 The m parameter of the switching function
=12

#other distances to check vs E240
#LYS 55 NZ
The ALPHARMSD action with label alpha_rmsd calculates the following quantities:
 Quantity   
 Description  
alpha_rmsd.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha_rmsd.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=816,2244
#ARG 80 CZ
The DISTANCE action with label d2 calculates a scalar quantityd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1254,2244
#GLN 68 CD
The DISTANCE action with label d3 calculates a scalar quantityd4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1033,2244
#ARG 74 CZ
The DISTANCE action with label d4 calculates a scalar quantityd5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1143,2244
# distance between CZ-R76 and OE1 and OE2 of E240
The DISTANCE action with label d5 calculates a scalar quantityd6: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1178,2245
The DISTANCE action with label d6 calculates a scalar quantityd7: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1178,2246
# distance between NH1-R76 and OE1 and OE2 of E240
The DISTANCE action with label d7 calculates a scalar quantityd8: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1179,2245
The DISTANCE action with label d8 calculates a scalar quantityd9: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1179,2246
# distance between NH2-R76 and OE1 and OE2 of E240
The DISTANCE action with label d9 calculates a scalar quantityd10: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1182,2245
The DISTANCE action with label d10 calculates a scalar quantityd11: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1182,2246
# distance between HZ1-K55 and OE1 and OE2 of E240
The DISTANCE action with label d11 calculates a scalar quantityd12: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=817,2245
The DISTANCE action with label d12 calculates a scalar quantityd13: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=817,2246
# distance between HZ2-K55 and OE1 and OE2 of E240
The DISTANCE action with label d13 calculates a scalar quantityd14: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=818,2245
The DISTANCE action with label d14 calculates a scalar quantityd15: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=818,2246
# distance between HZ3-K55 and OE1 and OE2 of E240
The DISTANCE action with label d15 calculates a scalar quantityd16: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=819,2245
The DISTANCE action with label d16 calculates a scalar quantityd17: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=819,2246
# distance between NZ-K55 and OE1 and OE2 of E240
The DISTANCE action with label d17 calculates a scalar quantityd18: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=816,2245
The DISTANCE action with label d18 calculates a scalar quantityd19: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=816,2246
# distance between CZ-R74 and OE1 and OE2 of E240
The DISTANCE action with label d19 calculates a scalar quantityd20: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1143,2245
The DISTANCE action with label d20 calculates a scalar quantityd21: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1143,2246
# distance between NH1-R74 and OE1 and OE2 of E240
The DISTANCE action with label d21 calculates a scalar quantityd22: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1144,2245
The DISTANCE action with label d22 calculates a scalar quantityd23: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1144,2246
# distance between NH2-R74 and OE1 and OE2 of E240
The DISTANCE action with label d23 calculates a scalar quantityd24: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1147,2245
The DISTANCE action with label d24 calculates a scalar quantityd25: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1147,2246
#distance between CZ-R80 and OE1 and OE2 of E240
The DISTANCE action with label d25 calculates a scalar quantityd26: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1254,2245
The DISTANCE action with label d26 calculates a scalar quantityd27: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1254,2246
#distance between NH1-R80 and OE1 and OE2 of E240
The DISTANCE action with label d27 calculates a scalar quantityd28: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1255,2245
The DISTANCE action with label d28 calculates a scalar quantityd29: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1255,2246
# distance between NH2-80 and OE1 and OE2 of E240
The DISTANCE action with label d29 calculates a scalar quantityd30: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1258,2245
The DISTANCE action with label d30 calculates a scalar quantityd31: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1258,2246

#angles to check for helix orientation
#CA E246; CA Q239; CA R76
The DISTANCE action with label d31 calculates a scalar quantitya1: 
ANGLE
Calculate an angle. More details
 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=2333,2219,1165
#CA E246; CA T237; CA R76
The ANGLE action with label a1 calculates a scalar quantitya2: 
ANGLE
Calculate an angle. More details
 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=2333,2191,1165


#to monitor the saltbridge contact between NH1,NH2 of R76 and   OE1,OE2 and O of E240 
The ANGLE action with label a2 calculates a scalar quantitycn1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1179,1180,1181,1182,1183,1184,1186 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2245,2246,2248 
D_0
 The d_0 parameter of the switching function
=0.19 
R_0
The r_0 parameter of the switching function
=0.30 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=12

## C-beta and C-alpha of R76 and C-alpha and C-beta of E240 to see the orientation of helix
The COORDINATION action with label cn1 calculates a scalar quantityt1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1165,1167,2236,2238
# C-beta and C-alpha of R76 and C-alpha and C-beta of E232 to see the orientation of helix
The TORSION action with label t1 calculates a scalar quantityt2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1165,1167,2109,211

#based on distance distribution of the models using the two templates (max dist)
The TORSION action with label t2 calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1 
AT
the positions of the wall
=1.7 
KAPPA
the force constant for the wall
=10000.0
#LOWER_WALLS ARG=d1 AT=0.2 KAPPA=1000.0

metad: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=2.5 
SIGMA
the widths of the Gaussian hills
=0.1 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.00 
GRID_MIN
the lower bounds for the grid
=0.1 
GRID_MAX
the upper bounds for the grid
=2.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.05



The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,metad.bias,ab-psi,ab-phi,alpha_rmsd,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,a1,a2,cn1,t1,t2 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=500