PLUMED-NEST

Project ID: plumID:22.000
Source: plumed-common-1.dat
Originally used with PLUMED version: 2.5
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=nm 
TIME
the units of time
=ps  
ENERGY
the units of energy
=kj/mol
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
=1.pdb
RANDOM_EXCHANGES
Set random pattern for exchanges. More details

hbond: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=5568,5504 
SWITCH1
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT1
A weight value for a given contact, by default is 1
=0.09091 
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=5546,5491 
SWITCH2
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT2
A weight value for a given contact, by default is 1
=0.09091 
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=5524,5471 
SWITCH3
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT3
A weight value for a given contact, by default is 1
=0.09091 
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=5505,5452 
SWITCH4
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT4
A weight value for a given contact, by default is 1
=0.09091 
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=5492,5438 
SWITCH5
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT5
A weight value for a given contact, by default is 1
=0.09091 
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=5472,5419 
SWITCH6
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT6
A weight value for a given contact, by default is 1
=0.09091 
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=5453,5403 
SWITCH7
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT7
A weight value for a given contact, by default is 1
=0.09091 
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=5439,5384 
SWITCH8
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT8
A weight value for a given contact, by default is 1
=0.09091 
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=5420,5368 
SWITCH9
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT9
A weight value for a given contact, by default is 1
=0.09091 
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=5404,5354 
SWITCH10
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT10
A weight value for a given contact, by default is 1
=0.09091 
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=5385,5344 
SWITCH11
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} 
WEIGHT11
A weight value for a given contact, by default is 1
=0.09091 
SUM
 calculate the sum of all the contacts in the input
 

The CONTACTMAP action with label hbond calculates the following quantities:
 Quantity   
 Description  
hbond.contact
By not using SUM or CMDIST each contact will be stored in a componentantibeta: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=3788,5453 
SWITCH1
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.42} 
WEIGHT1
A weight value for a given contact, by default is 1
=0.09091 
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=3788,5471 
SWITCH2
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} 
WEIGHT2
A weight value for a given contact, by default is 1
=0.09091 
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=3788,5472 
SWITCH3
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.39} 
WEIGHT3
A weight value for a given contact, by default is 1
=0.09091 
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=3788,5487 
SWITCH4
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.34} 
WEIGHT4
A weight value for a given contact, by default is 1
=0.09091 
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=3769,5487 
SWITCH5
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} 
WEIGHT5
A weight value for a given contact, by default is 1
=0.09091 
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=3768,5487 
SWITCH6
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31} 
WEIGHT6
A weight value for a given contact, by default is 1
=0.09091 
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=3768,5488 
SWITCH7
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} 
WEIGHT7
A weight value for a given contact, by default is 1
=0.09091 
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=3768,5505 
SWITCH8
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31} 
WEIGHT8
A weight value for a given contact, by default is 1
=0.09091 
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=3768,5523 
SWITCH9
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.37} 
WEIGHT9
A weight value for a given contact, by default is 1
=0.09091 
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=3747,5505 
SWITCH10
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.44} 
WEIGHT10
A weight value for a given contact, by default is 1
=0.09091 
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=3747,5523 
SWITCH11
The switching functions to use for each of the contacts in your map
={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.29} 
WEIGHT11
A weight value for a given contact, by default is 1
=0.09091 
SUM
 calculate the sum of all the contacts in the input

The CONTACTMAP action with label antibeta calculates the following quantities:
 Quantity   
 Description  
antibeta.contact
By not using SUM or CMDIST each contact will be stored in a componentanti1: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.1  
STRANDS_CUTOFF
If 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 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=inter
The ANTIBETARMSD action with label anti1 calculates the following quantities:
 Quantity   
 Description  
anti1.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti1.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdanti2: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=430,431,432,433,434,435,32,33,34,35,36,37 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.1  
STRANDS_CUTOFF
If 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 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=inter

The ANTIBETARMSD action with label anti2 calculates the following quantities:
 Quantity   
 Description  
anti2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdinteract: 
COORDINATION
Calculate coordination numbers. More details
  
GROUPA
First list of atoms
=3731,3733,3735,3737,3741,3745,3746,3747,3749,3751,3754,3757,3760,3763,3767,3768,3769,3771,3773,3776,3778,3782,3786,3787,3788,3790,3793,3794,4515,4517,4519,4522,4525,4528,4531,4535,4536,4537,4539,4541,4545,4546,4547,4549,4551,4554,4556,4560,4564,4565,4566,4567,4570,4572,4575,4578,4579,4580,4582,4584,4588,4589,4590,4592,4594,4597,4599,4603,4607,4608  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5472,5474,5476,5478,5482,5486,5487,5488,5490,5492,5495,5498,5499,5503,5504,5505,5507,5509,5512,5514,5518,5522,5523,5524,5526,5528,5531,5534,5540,5544,5545  
R_0
The r_0 parameter of the switching function
=0.45

The COORDINATION action with label interact calculates a scalar quantityalpha: 
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
=28-39 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.1 
D_0
 The d_0 parameter of the switching function
=0.02
The ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Description  
alpha.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdapp_head: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5371,5387
app_tail: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5548,5570
distance: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=app_head,app_tail
The DISTANCE action with label distance calculates a scalar quantity