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

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=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
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=1-1988 ENTITY1the 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
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1178,2244

#to monitor only
#helical content of the region - psi angle
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-239the four atoms that are required to calculate the psi dihedral for residue 239. Click here for more information.  REFERENCE1the reference values for each of the torsional angles=-0.79
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-240the four atoms that are required to calculate the psi dihedral for residue 240. Click here for more information.  REFERENCE2the reference values for each of the torsional angles=-0.79
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-241the four atoms that are required to calculate the psi dihedral for residue 241. Click here for more information.  REFERENCE3the reference values for each of the torsional angles=-0.79
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-242the four atoms that are required to calculate the psi dihedral for residue 242. Click here for more information.  REFERENCE4the reference values for each of the torsional angles=-0.79
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-243the four atoms that are required to calculate the psi dihedral for residue 243. Click here for more information.  REFERENCE5the reference values for each of the torsional angles=-0.79
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-244the four atoms that are required to calculate the psi dihedral for residue 244. Click here for more information.  REFERENCE6the reference values for each of the torsional angles=-0.79
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-245the four atoms that are required to calculate the psi dihedral for residue 245. Click here for more information.  REFERENCE7the reference values for each of the torsional angles=-0.79
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-246the four atoms that are required to calculate the psi dihedral for residue 246. Click here for more information.  REFERENCE8the reference values for each of the torsional angles=-0.79
LABELa label for the action so that its output can be referenced in the input to other actions=ab-psiThe ALPHABETA action with label ab-psi calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=@psi-239 REFERENCE1=-0.79
# ATOMS2=@psi-240 REFERENCE2=-0.79
# ATOMS3=@psi-241 REFERENCE3=-0.79
# ATOMS4=@psi-242 REFERENCE4=-0.79
# ATOMS5=@psi-243 REFERENCE5=-0.79
# ATOMS6=@psi-244 REFERENCE6=-0.79
# ATOMS7=@psi-245 REFERENCE7=-0.79
# ATOMS8=@psi-246 REFERENCE8=-0.79
# LABEL=ab-psi
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab-psi_torsionsThe TORSION action with label ab-psi_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-239the four atoms that are required to calculate the psi dihedral for residue 239. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-240the four atoms that are required to calculate the psi dihedral for residue 240. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-241the four atoms that are required to calculate the psi dihedral for residue 241. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@psi-242the four atoms that are required to calculate the psi dihedral for residue 242. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-243the four atoms that are required to calculate the psi dihedral for residue 243. Click here for more information.      # Action input conctinues with 3 further ATOMSn keywords, 
ab-psi_refThe CONSTANT action with label ab-psi_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.79,-0.79,-0.79,-0.79,-0.79,-0.79,-0.79,-0.79
ab-psi_coeffThe CONSTANT action with label ab-psi_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1
ab-psi_combThe COMBINE action with label ab-psi_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab-psi_torsions,ab-psi_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab-psi_cosThe CUSTOM action with label ab-psi_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab-psi_comb,ab-psi_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab-psiThe SUM action with label ab-psi calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-psi
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=ab-psi_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- #helical content of the region phi angle
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-239the four atoms that are required to calculate the phi dihedral for residue 239. Click here for more information.  REFERENCE1the reference values for each of the torsional angles=-1.05
ATOMS2the atoms involved for each of the torsions you wish to calculate=@phi-240the four atoms that are required to calculate the phi dihedral for residue 240. Click here for more information.  REFERENCE2the reference values for each of the torsional angles=-1.05
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-241the four atoms that are required to calculate the phi dihedral for residue 241. Click here for more information.  REFERENCE3the reference values for each of the torsional angles=-1.05
ATOMS4the atoms involved for each of the torsions you wish to calculate=@phi-242the four atoms that are required to calculate the phi dihedral for residue 242. Click here for more information.  REFERENCE4the reference values for each of the torsional angles=-1.05
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-243the four atoms that are required to calculate the phi dihedral for residue 243. Click here for more information.  REFERENCE5the reference values for each of the torsional angles=-1.05
ATOMS6the atoms involved for each of the torsions you wish to calculate=@phi-244the four atoms that are required to calculate the phi dihedral for residue 244. Click here for more information.  REFERENCE6the reference values for each of the torsional angles=-1.05
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-245the four atoms that are required to calculate the phi dihedral for residue 245. Click here for more information.  REFERENCE7the reference values for each of the torsional angles=-1.05
ATOMS8the atoms involved for each of the torsions you wish to calculate=@phi-246the four atoms that are required to calculate the phi dihedral for residue 246. Click here for more information.  REFERENCE8the reference values for each of the torsional angles=-1.05
LABELa label for the action so that its output can be referenced in the input to other actions=ab-phiThe ALPHABETA action with label ab-phi calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=@phi-239 REFERENCE1=-1.05
# ATOMS2=@phi-240 REFERENCE2=-1.05
# ATOMS3=@phi-241 REFERENCE3=-1.05
# ATOMS4=@phi-242 REFERENCE4=-1.05
# ATOMS5=@phi-243 REFERENCE5=-1.05
# ATOMS6=@phi-244 REFERENCE6=-1.05
# ATOMS7=@phi-245 REFERENCE7=-1.05
# ATOMS8=@phi-246 REFERENCE8=-1.05
# LABEL=ab-phi
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab-phi_torsionsThe TORSION action with label ab-phi_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@phi-239the four atoms that are required to calculate the phi dihedral for residue 239. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@phi-240the four atoms that are required to calculate the phi dihedral for residue 240. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@phi-241the four atoms that are required to calculate the phi dihedral for residue 241. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@phi-242the four atoms that are required to calculate the phi dihedral for residue 242. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@phi-243the four atoms that are required to calculate the phi dihedral for residue 243. Click here for more information.      # Action input conctinues with 3 further ATOMSn keywords, 
ab-phi_refThe CONSTANT action with label ab-phi_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-1.05,-1.05,-1.05,-1.05,-1.05,-1.05,-1.05,-1.05
ab-phi_coeffThe CONSTANT action with label ab-phi_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1
ab-phi_combThe COMBINE action with label ab-phi_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab-phi_torsions,ab-phi_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab-phi_cosThe CUSTOM action with label ab-phi_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab-phi_comb,ab-phi_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab-phiThe SUM action with label ab-phi calculates the following quantities:
 Quantity   
 Type   
 Description  
ab-phi
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=ab-phi_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#alphaRMSD
alpha_rmsdThe ALPHARMSD action with label alpha_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_rmsd
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix.  If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut. More details RESIDUESthis 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_0The 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
# PLUMED interprets the command:
# alpha_rmsd: ALPHARMSD RESIDUES=239-246 TYPE=OPTIMAL R_0=0.08 D_0=0.0 NN=8 MM=12
# as follows (Click the red comment above to revert to the short version of the input):
alpha_rmsd_rmsdThe SECONDARY_STRUCTURE_RMSD action with label alpha_rmsd_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_rmsd_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 SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673 ATOMSthis is the full list of atoms that we are investigating=2217,2219,2221,2232,2233,2234,2236,2238,2247,2248,2249,2251,2253,2262,2263,2264,2266,2268,2278,2279,2280,2282,2284,2293,2294,2295,2297,2299,2308,2309,2310,2312,2314,2327,2328,2329,2331,2333,2342,2343 TYPE the manner in which RMSD alignment is performed=OPTIMAL
alpha_rmsd_ltThe LESS_THAN action with label alpha_rmsd_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_rmsd_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=alpha_rmsd_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
alpha_rmsdThe SUM action with label alpha_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_rmsd
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=alpha_rmsd_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#other distances to check vs E240
#LYS 55 NZ
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=816,2244
#ARG 80 CZ
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1254,2244
#GLN 68 CD
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1033,2244
#ARG 74 CZ
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1143,2244
# distance between CZ-R76 and OE1 and OE2 of E240
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1178,2245
d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1178,2246
# distance between NH1-R76 and OE1 and OE2 of E240
d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1179,2245
d9The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Type   
 Description  
d9
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1179,2246
# distance between NH2-R76 and OE1 and OE2 of E240
d10The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Type   
 Description  
d10
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1182,2245
d11The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Type   
 Description  
d11
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1182,2246
# distance between HZ1-K55 and OE1 and OE2 of E240
d12The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Type   
 Description  
d12
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=817,2245
d13The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Type   
 Description  
d13
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=817,2246
# distance between HZ2-K55 and OE1 and OE2 of E240
d14The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Type   
 Description  
d14
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=818,2245
d15The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Type   
 Description  
d15
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=818,2246
# distance between HZ3-K55 and OE1 and OE2 of E240
d16The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Type   
 Description  
d16
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=819,2245
d17The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Type   
 Description  
d17
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=819,2246
# distance between NZ-K55 and OE1 and OE2 of E240
d18The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Type   
 Description  
d18
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=816,2245
d19The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Type   
 Description  
d19
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=816,2246
# distance between CZ-R74 and OE1 and OE2 of E240
d20The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Type   
 Description  
d20
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1143,2245
d21The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Type   
 Description  
d21
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1143,2246
# distance between NH1-R74 and OE1 and OE2 of E240
d22The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Type   
 Description  
d22
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1144,2245
d23The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Type   
 Description  
d23
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1144,2246
# distance between NH2-R74 and OE1 and OE2 of E240
d24The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Type   
 Description  
d24
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1147,2245
d25The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Type   
 Description  
d25
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1147,2246
#distance between CZ-R80 and OE1 and OE2 of E240
d26The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Type   
 Description  
d26
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1254,2245
d27The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Type   
 Description  
d27
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1254,2246
#distance between NH1-R80 and OE1 and OE2 of E240
d28The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Type   
 Description  
d28
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1255,2245
d29The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Type   
 Description  
d29
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1255,2246
# distance between NH2-80 and OE1 and OE2 of E240
d30The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Type   
 Description  
d30
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1258,2245
d31The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Type   
 Description  
d31
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1258,2246

#angles to check for helix orientation
#CA E246; CA Q239; CA R76
a1The ANGLE action with label a1 calculates the following quantities:
 Quantity   
 Type   
 Description  
a1
scalar
the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=2333,2219,1165
#CA E246; CA T237; CA R76
a2The ANGLE action with label a2 calculates the following quantities:
 Quantity   
 Type   
 Description  
a2
scalar
the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe 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 
cn1The COORDINATION action with label cn1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1179,1180,1181,1182,1183,1184,1186 GROUPBSecond 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_0The 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
t1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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
t2The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1165,1167,2109,211

#based on distance distribution of the models using the two templates (max dist)
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=1.7 KAPPAthe force constant for the wall=10000.0
#LOWER_WALLS ARG=d1 AT=0.2 KAPPA=1000.0

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=d1 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=2.5 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.00 GRID_MINthe lower bounds for the grid=0.1 GRID_MAXthe upper bounds for the grid=2.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05



PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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 FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500 
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500