PLUMED-NEST-TEST-SITE

Project ID: plumID:22.024
Source: dka/plumed.dat
Originally used with PLUMED version: 2.6
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

# RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein 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=1-1914
# DEBUG DETAILED_TIMERS

# AB over backbone
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-99the four atoms that are required to calculate the phi dihedral for residue 99. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=pi
    ATOMS2the atoms involved for each of the torsions you wish to calculate=@phi-100the four atoms that are required to calculate the phi dihedral for residue 100. Click here for more information. 
    ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-101the four atoms that are required to calculate the phi dihedral for residue 101. Click here for more information. 
    ATOMS4the atoms involved for each of the torsions you wish to calculate=@phi-102the four atoms that are required to calculate the phi dihedral for residue 102. Click here for more information. 
    ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-103the four atoms that are required to calculate the phi dihedral for residue 103. Click here for more information. 
    ATOMS6the atoms involved for each of the torsions you wish to calculate=@phi-104the four atoms that are required to calculate the phi dihedral for residue 104. Click here for more information. 
    ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-105the four atoms that are required to calculate the phi dihedral for residue 105. Click here for more information. 
    ATOMS8the atoms involved for each of the torsions you wish to calculate=@phi-106the four atoms that are required to calculate the phi dihedral for residue 106. Click here for more information. 
    ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-107the four atoms that are required to calculate the phi dihedral for residue 107. Click here for more information. 
    ATOMS10the atoms involved for each of the torsions you wish to calculate=@phi-108the four atoms that are required to calculate the phi dihedral for residue 108. Click here for more information. 
    ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-109the four atoms that are required to calculate the phi dihedral for residue 109. Click here for more information. 
    ATOMS12the atoms involved for each of the torsions you wish to calculate=@phi-110the four atoms that are required to calculate the phi dihedral for residue 110. Click here for more information. 
    ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-111the four atoms that are required to calculate the phi dihedral for residue 111. Click here for more information. 
    ATOMS14the atoms involved for each of the torsions you wish to calculate=@phi-112the four atoms that are required to calculate the phi dihedral for residue 112. Click here for more information. 
    ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-113the four atoms that are required to calculate the phi dihedral for residue 113. Click here for more information. 
    ATOMS16the atoms involved for each of the torsions you wish to calculate=@phi-114the four atoms that are required to calculate the phi dihedral for residue 114. Click here for more information. 
    ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-115the four atoms that are required to calculate the phi dihedral for residue 115. Click here for more information. 
    ATOMS18the atoms involved for each of the torsions you wish to calculate=@phi-116the four atoms that are required to calculate the phi dihedral for residue 116. Click here for more information. 
    ATOMS19the atoms involved for each of the torsions you wish to calculate=@phi-117the four atoms that are required to calculate the phi dihedral for residue 117. Click here for more information. 
    ATOMS20the atoms involved for each of the torsions you wish to calculate=@psi-99the four atoms that are required to calculate the psi dihedral for residue 99. Click here for more information. 
    ATOMS21the atoms involved for each of the torsions you wish to calculate=@psi-100the four atoms that are required to calculate the psi dihedral for residue 100. Click here for more information. 
    ATOMS22the atoms involved for each of the torsions you wish to calculate=@psi-101the four atoms that are required to calculate the psi dihedral for residue 101. Click here for more information. 
    ATOMS23the atoms involved for each of the torsions you wish to calculate=@psi-102the four atoms that are required to calculate the psi dihedral for residue 102. Click here for more information. 
    ATOMS24the atoms involved for each of the torsions you wish to calculate=@psi-103the four atoms that are required to calculate the psi dihedral for residue 103. Click here for more information. 
    ATOMS25the atoms involved for each of the torsions you wish to calculate=@psi-104the four atoms that are required to calculate the psi dihedral for residue 104. Click here for more information. 
    ATOMS26the atoms involved for each of the torsions you wish to calculate=@psi-105the four atoms that are required to calculate the psi dihedral for residue 105. Click here for more information. 
    ATOMS27the atoms involved for each of the torsions you wish to calculate=@psi-106the four atoms that are required to calculate the psi dihedral for residue 106. Click here for more information. 
    ATOMS28the atoms involved for each of the torsions you wish to calculate=@psi-107the four atoms that are required to calculate the psi dihedral for residue 107. Click here for more information. 
    ATOMS29the atoms involved for each of the torsions you wish to calculate=@psi-108the four atoms that are required to calculate the psi dihedral for residue 108. Click here for more information. 
    ATOMS30the atoms involved for each of the torsions you wish to calculate=@psi-109the four atoms that are required to calculate the psi dihedral for residue 109. Click here for more information. 
    ATOMS31the atoms involved for each of the torsions you wish to calculate=@psi-110the four atoms that are required to calculate the psi dihedral for residue 110. Click here for more information. 
    ATOMS32the atoms involved for each of the torsions you wish to calculate=@psi-111the four atoms that are required to calculate the psi dihedral for residue 111. Click here for more information. 
    ATOMS33the atoms involved for each of the torsions you wish to calculate=@psi-112the four atoms that are required to calculate the psi dihedral for residue 112. Click here for more information. 
    ATOMS34the atoms involved for each of the torsions you wish to calculate=@psi-113the four atoms that are required to calculate the psi dihedral for residue 113. Click here for more information. 
    ATOMS35the atoms involved for each of the torsions you wish to calculate=@psi-114the four atoms that are required to calculate the psi dihedral for residue 114. Click here for more information. 
    ATOMS36the atoms involved for each of the torsions you wish to calculate=@psi-115the four atoms that are required to calculate the psi dihedral for residue 115. Click here for more information. 
    ATOMS37the atoms involved for each of the torsions you wish to calculate=@psi-116the four atoms that are required to calculate the psi dihedral for residue 116. Click here for more information. 
    ATOMS38the atoms involved for each of the torsions you wish to calculate=@psi-117the four atoms that are required to calculate the psi dihedral for residue 117. Click here for more information. 
    LABELa label for the action so that its output can be referenced in the input to other actions=abbbThe ALPHABETA action with label abbb calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
#     ATOMS1=@phi-99 REFERENCE=pi
#     ATOMS2=@phi-100
#     ATOMS3=@phi-101
#     ATOMS4=@phi-102
#     ATOMS5=@phi-103
#     ATOMS6=@phi-104
#     ATOMS7=@phi-105
#     ATOMS8=@phi-106
#     ATOMS9=@phi-107
#     ATOMS10=@phi-108
#     ATOMS11=@phi-109
#     ATOMS12=@phi-110
#     ATOMS13=@phi-111
#     ATOMS14=@phi-112
#     ATOMS15=@phi-113
#     ATOMS16=@phi-114
#     ATOMS17=@phi-115
#     ATOMS18=@phi-116
#     ATOMS19=@phi-117
#     ATOMS20=@psi-99
#     ATOMS21=@psi-100
#     ATOMS22=@psi-101
#     ATOMS23=@psi-102
#     ATOMS24=@psi-103
#     ATOMS25=@psi-104
#     ATOMS26=@psi-105
#     ATOMS27=@psi-106
#     ATOMS28=@psi-107
#     ATOMS29=@psi-108
#     ATOMS30=@psi-109
#     ATOMS31=@psi-110
#     ATOMS32=@psi-111
#     ATOMS33=@psi-112
#     ATOMS34=@psi-113
#     ATOMS35=@psi-114
#     ATOMS36=@psi-115
#     ATOMS37=@psi-116
#     ATOMS38=@psi-117
#     LABEL=abbb
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
abbb_torsionsThe TORSION action with label abbb_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb_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-99the four atoms that are required to calculate the phi dihedral for residue 99. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@phi-100the four atoms that are required to calculate the phi dihedral for residue 100. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@phi-101the four atoms that are required to calculate the phi dihedral for residue 101. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@phi-102the four atoms that are required to calculate the phi dihedral for residue 102. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@phi-103the four atoms that are required to calculate the phi dihedral for residue 103. Click here for more information.      # Action input conctinues with 33 further ATOMSn keywords, 
abbb_refThe CONSTANT action with label abbb_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb_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=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
abbb_coeffThe CONSTANT action with label abbb_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb_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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
abbb_combThe COMBINE action with label abbb_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb_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=abbb_torsions,abbb_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
abbb_cosThe CUSTOM action with label abbb_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb_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=abbb_comb,abbb_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
abbbThe SUM action with label abbb calculates the following quantities:
 Quantity   
 Type   
 Description  
abbb
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=abbb_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# AB over sidechains
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=@chi1-99the four atoms that are required to calculate the chi1 dihedral for residue 99. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=pi
    ATOMS2the atoms involved for each of the torsions you wish to calculate=@chi1-100the four atoms that are required to calculate the chi1 dihedral for residue 100. Click here for more information. 
    ATOMS3the atoms involved for each of the torsions you wish to calculate=@chi1-101the four atoms that are required to calculate the chi1 dihedral for residue 101. Click here for more information. 
    ATOMS4the atoms involved for each of the torsions you wish to calculate=@chi1-103the four atoms that are required to calculate the chi1 dihedral for residue 103. Click here for more information. 
    ATOMS5the atoms involved for each of the torsions you wish to calculate=@chi1-104the four atoms that are required to calculate the chi1 dihedral for residue 104. Click here for more information. 
    ATOMS6the atoms involved for each of the torsions you wish to calculate=@chi1-105the four atoms that are required to calculate the chi1 dihedral for residue 105. Click here for more information. 
    ATOMS7the atoms involved for each of the torsions you wish to calculate=@chi1-106the four atoms that are required to calculate the chi1 dihedral for residue 106. Click here for more information. 
    ATOMS8the atoms involved for each of the torsions you wish to calculate=@chi1-107the four atoms that are required to calculate the chi1 dihedral for residue 107. Click here for more information. 
    ATOMS9the atoms involved for each of the torsions you wish to calculate=@chi1-108the four atoms that are required to calculate the chi1 dihedral for residue 108. Click here for more information. 
    ATOMS10the atoms involved for each of the torsions you wish to calculate=@chi1-109the four atoms that are required to calculate the chi1 dihedral for residue 109. Click here for more information. 
    ATOMS11the atoms involved for each of the torsions you wish to calculate=@chi1-110the four atoms that are required to calculate the chi1 dihedral for residue 110. Click here for more information. 
    ATOMS12the atoms involved for each of the torsions you wish to calculate=@chi1-111the four atoms that are required to calculate the chi1 dihedral for residue 111. Click here for more information. 
    ATOMS13the atoms involved for each of the torsions you wish to calculate=@chi1-112the four atoms that are required to calculate the chi1 dihedral for residue 112. Click here for more information. 
    ATOMS14the atoms involved for each of the torsions you wish to calculate=@chi1-113the four atoms that are required to calculate the chi1 dihedral for residue 113. Click here for more information. 
    ATOMS15the atoms involved for each of the torsions you wish to calculate=@chi1-114the four atoms that are required to calculate the chi1 dihedral for residue 114. Click here for more information. 
    ATOMS16the atoms involved for each of the torsions you wish to calculate=@chi1-115the four atoms that are required to calculate the chi1 dihedral for residue 115. Click here for more information. 
    ATOMS17the atoms involved for each of the torsions you wish to calculate=@chi1-116the four atoms that are required to calculate the chi1 dihedral for residue 116. Click here for more information. 
    ATOMS18the atoms involved for each of the torsions you wish to calculate=@chi1-117the four atoms that are required to calculate the chi1 dihedral for residue 117. Click here for more information. 
    LABELa label for the action so that its output can be referenced in the input to other actions=abscThe ALPHABETA action with label absc calculates the following quantities:
 Quantity   
 Type   
 Description  
absc
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
#     ATOMS1=@chi1-99 REFERENCE=pi
#     ATOMS2=@chi1-100
#     ATOMS3=@chi1-101
#     ATOMS4=@chi1-103
#     ATOMS5=@chi1-104
#     ATOMS6=@chi1-105
#     ATOMS7=@chi1-106
#     ATOMS8=@chi1-107
#     ATOMS9=@chi1-108
#     ATOMS10=@chi1-109
#     ATOMS11=@chi1-110
#     ATOMS12=@chi1-111
#     ATOMS13=@chi1-112
#     ATOMS14=@chi1-113
#     ATOMS15=@chi1-114
#     ATOMS16=@chi1-115
#     ATOMS17=@chi1-116
#     ATOMS18=@chi1-117
#     LABEL=absc
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
absc_torsionsThe TORSION action with label absc_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
absc_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=@chi1-99the four atoms that are required to calculate the chi1 dihedral for residue 99. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@chi1-100the four atoms that are required to calculate the chi1 dihedral for residue 100. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@chi1-101the four atoms that are required to calculate the chi1 dihedral for residue 101. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@chi1-103the four atoms that are required to calculate the chi1 dihedral for residue 103. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@chi1-104the four atoms that are required to calculate the chi1 dihedral for residue 104. Click here for more information.      # Action input conctinues with 13 further ATOMSn keywords, 
absc_refThe CONSTANT action with label absc_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
absc_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=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
absc_coeffThe CONSTANT action with label absc_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
absc_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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
absc_combThe COMBINE action with label absc_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
absc_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=absc_torsions,absc_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
absc_cosThe CUSTOM action with label absc_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
absc_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=absc_comb,absc_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
abscThe SUM action with label absc calculates the following quantities:
 Quantity   
 Type   
 Description  
absc
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=absc_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# Alpha-helix for CDR
helixThe ALPHARMSD action with label helix calculates the following quantities:
 Quantity   
 Type   
 Description  
helix
vector
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
helix_lessthan
scalar
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold: 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=99-117 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12}
# PLUMED interprets the command:
# helix: ALPHARMSD RESIDUES=99-117 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}
# as follows (Click the red comment above to revert to the short version of the input):
helixThe SECONDARY_STRUCTURE_RMSD action with label helix calculates the following quantities:
 Quantity   
 Type   
 Description  
helix
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=1465,1467,1469,1475,1476,1477,1479,1481,1499,1500,1501,1503,1505,1519,1520,1521,1525,1527,1533,1534,1535,1537,1539,1547,1548,1549,1551,1553,1564,1565,1566,1568,1570,1579,1580,1581,1583,1585,1595,1596,1597,1599,1601,1611,1612,1613,1615,1617,1625,1626,1627,1629,1631,1644,1645,1646,1648,1650,1661,1662,1663,1665,1667,1675,1676,1677,1679,1681,1689,1690,1691,1693,1695,1704,1705,1706,1708,1710,1725,1726,1727,1729,1731,1737,1738,1739,1741,1743,1758,1759,1760,1762,1764,1782,1783 TYPE the manner in which RMSD alignment is performed=DRMSD 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 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 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     # Action input conctinues with 9 further SEGMENTn keywords, 
helix_ltThe LESS_THAN action with label helix_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_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=helix SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 NN=8 MM=12}
helix_lessthanThe SUM action with label helix_lessthan calculates the following quantities:
 Quantity   
 Type   
 Description  
helix_lessthan
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=helix_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# Beta-sheet for CDR
antiThe ANTIBETARMSD action with label anti calculates the following quantities:
 Quantity   
 Type   
 Description  
anti
vector
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
anti_lessthan
scalar
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold: 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=99-117 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12}
anti: 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=99-117 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12}  STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# anti: ANTIBETARMSD RESIDUES=99-117 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}
# as follows (Click the red comment above to revert to the short version of the input):
antiThe SECONDARY_STRUCTURE_RMSD action with label anti calculates the following quantities:
 Quantity   
 Type   
 Description  
anti
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=1465,1467,1469,1475,1476,1477,1479,1481,1499,1500,1501,1503,1505,1519,1520,1521,1525,1527,1533,1534,1535,1537,1539,1547,1548,1549,1551,1553,1564,1565,1566,1568,1570,1579,1580,1581,1583,1585,1595,1596,1597,1599,1601,1611,1612,1613,1615,1617,1625,1626,1627,1629,1631,1644,1645,1646,1648,1650,1661,1662,1663,1665,1667,1675,1676,1677,1679,1681,1689,1690,1691,1693,1695,1704,1705,1706,1708,1710,1725,1726,1727,1729,1731,1737,1738,1739,1741,1743,1758,1759,1760,1762,1764,1782,1783 TYPE the manner in which RMSD alignment is performed=DRMSD 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=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT5this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 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 73 further SEGMENTn keywords, 
anti_ltThe LESS_THAN action with label anti_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
anti_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=anti SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 NN=8 MM=12}
anti_lessthanThe SUM action with label anti_lessthan calculates the following quantities:
 Quantity   
 Type   
 Description  
anti_lessthan
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=anti_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=pbmetadThe PBMETAD action with label pbmetad calculates the following quantities:
 Quantity   
 Type   
 Description  
pbmetad.bias
scalar
the instantaneous value of the bias potential
    ARGthe labels of the scalars on which the bias will act=abbb,absc,helix.lessthan,anti.lessthan
    PACEthe frequency for hill addition, one for all biases=500 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=24 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
    SIGMAthe widths of the Gaussian hills=1.5,0.5,2.0,1.5
    FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_abbb,HILLS_absc,HILLS_helix,HILLS_anti
    GRID_MINthe lower bounds for the grid=-1,-1,-1,-1
    GRID_MAXthe upper bounds for the grid=50,20,100,100
    GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_anti
    #GRID_RFILES=GRID_abbb,GRID_absc,GRID_helix,GRID_anti
    GRID_WSTRIDEfrequency for dumping the grid=10000
... PBMETAD

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=BIAS ARGthe labels of the values that you would like to print to the file=abbb,absc,helix.lessthan,anti.lessthan,pbmetad.bias