PLUMED-NEST

Project ID: plumID:23.006
Source: 1OSL_CV_analsyis/plumed_print.dat
Originally used with PLUMED version: 2.7.2
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

# Activate MOLINFO functionalities
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
=1osl_C52V_GMX_new_numbering.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
# alphaRMSD
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
=87-93,149-155 
# Define the area you want to analyse
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 thresholdProtein_COM: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1145-3076 # not used, DBD plus part of core
DNA_center: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=255-257,287-289,827-829,859-861 # P and OP of central two basepairs 
# Define the distance between the hinges and the DNA center
hingeA: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1923,1925,1945-1947,1949,1962-1963,1965,1971-1973,1975,1988-1990,1992,2005,2007,2009,2024,2026,2028,2041,2042 # hinge backbone atoms (N,C,O,CA)
hingeB: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=2887,2889,2909,2911,2913,2925,2927,2929,2935,2937,2939,2952,2954,2956,2969,2971,2973,2988,2990,2992,2998,2999 # hinge backbone atoms (N,C,O,CA)
distA: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=hingeA,DNA_center
The DISTANCE action with label distA calculates a scalar quantitydistB: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=hingeB,DNA_center
The DISTANCE action with label distB calculates a scalar quantitydistH: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=hingeA,hingeB

# define the DNA bending vector
The DISTANCE action with label distH calculates a scalar quantityp1_l: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-28,1111-1144 # first (fourth) bp
p1_r: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=539-600 # last (21st) bp
DNA_bent: 
ANGLE
Calculate an angle. More details
 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=p1_l,DNA_center,p1_r

# check for native contacts
The ANGLE action with label DNA_bent calculates a scalar quantity
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
=1239,938 
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.5230 }
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=1262,906 
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4182 }
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=1401,904 
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3135 }
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1420,176 
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2687 }
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=1463,938 
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4656 }
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=1486,115 
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3112 }
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=1592,77 
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4396 }
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=2200,332 
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4943 }
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=2228,334 
SWITCH9
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3835 }
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=2369,366 
SWITCH10
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2899 }
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=2387,402 
SWITCH11
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2666 }
ATOMS12
the atoms involved in each of the contacts you wish to calculate
=2429,366 
SWITCH12
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4717 }
ATOMS13
the atoms involved in each of the contacts you wish to calculate
=2452,687 
SWITCH13
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2917 }
ATOMS14
the atoms involved in each of the contacts you wish to calculate
=2545,614 
SWITCH14
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4913 }
ATOMS15
the atoms involved in each of the contacts you wish to calculate
=1944,2917 
SWITCH15
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.5311 }
ATOMS16
the atoms involved in each of the contacts you wish to calculate
=1960,2917 
SWITCH16
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3087 }
ATOMS17
the atoms involved in each of the contacts you wish to calculate
=1965,2980 
SWITCH17
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3807 }
ATOMS18
the atoms involved in each of the contacts you wish to calculate
=1986,2917 
SWITCH18
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.6346 }
ATOMS19
the atoms involved in each of the contacts you wish to calculate
=1999,2921 
SWITCH19
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3000 }
ATOMS20
the atoms involved in each of the contacts you wish to calculate
=2018,2984 
SWITCH20
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3287 }
ATOMS21
the atoms involved in each of the contacts you wish to calculate
=2024,2984 
SWITCH21
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.6335 }
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cmap
SUM
 calculate the sum of all the contacts in the input
... CONTACTMAP

# check for native contacts, hinge
The CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Description  
cmap.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=1944,2917 
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.5311 }
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=1960,2917 
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3087 }
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=1965,2980 
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3807 }
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1986,2917 
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.6346 }
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=1999,2921 
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3000 }
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=2018,2984 
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3287 }
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=2024,2984 
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.6335 }
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cmap_hinge
SUM
 calculate the sum of all the contacts in the input
... CONTACTMAP

# check for native contacts, DNA
The CONTACTMAP action with label cmap_hinge calculates the following quantities:
 Quantity   
 Description  
cmap_hinge.contact
By not using SUM or CMDIST each contact will be stored in a component
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
=1239,938 
SWITCH1
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.5230 }
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=1262,906 
SWITCH2
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4182 }
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=1401,904 
SWITCH3
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3135 }
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=1420,176 
SWITCH4
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2687 }
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=1463,938 
SWITCH5
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4656 }
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=1486,115 
SWITCH6
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3112 }
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=1592,77 
SWITCH7
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4396 }
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=2200,332 
SWITCH8
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4943 }
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=2228,334 
SWITCH9
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.3835 }
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=2369,366 
SWITCH10
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2899 }
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=2387,402 
SWITCH11
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2666 }
ATOMS12
the atoms involved in each of the contacts you wish to calculate
=2429,366 
SWITCH12
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4717 }
ATOMS13
the atoms involved in each of the contacts you wish to calculate
=2452,687 
SWITCH13
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.2917 }
ATOMS14
the atoms involved in each of the contacts you wish to calculate
=2545,614 
SWITCH14
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.4913 }
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cmap_DNA
SUM
 calculate the sum of all the contacts in the input
... CONTACTMAP
# Print both collective variables on CVs file
The CONTACTMAP action with label cmap_DNA calculates the following quantities:
 Quantity   
 Description  
cmap_DNA.contact
By not using SUM or CMDIST each contact will be stored in a component
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cmap,alpha,DNA_bent,distH,distA,distB,cmap_DNA,cmap_hinge 
FILE
the name of the file on which to output these quantities
=CVs 
STRIDE
 the frequency with which the quantities of interest should be output
=1