Project ID: plumID:22.000
Source: plumed-common-3.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
tested onv2.9
tested onmaster
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
=3.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
=427,363
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
=405,346
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
=383,330
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
=364,311
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
=347,297
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
=331,278
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
=312,262
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
=298,243
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
=279,227
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
=263,213
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
=244,203
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

alpha:
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 app_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
=230,246 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
=407,429 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