PLUMED-NEST-TEST-SITE

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
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=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
The MOLINFO action with label  calculates somethingalphaThe ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha
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 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=87-93,149-155 
alpha: ALPHARMSDProbe the alpha helical content of a 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=87-93,149-155  NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 TYPE the manner in which RMSD alignment is performed=DRMSD
# PLUMED interprets the command:
# alpha: ALPHARMSD RESIDUES=87-93,149-155 
# as follows (Click the red comment above to revert to the short version of the input):
alpha_rmsdThe SECONDARY_STRUCTURE_RMSD action with label alpha_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_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=35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64 SEGMENT4this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69 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=1921,1923,1925,1943,1944,1945,1947,1949,1959,1960,1961,1963,1965,1969,1970,1971,1973,1975,1986,1987,1988,1990,1992,2003,2004,2005,2007,2009,2022,2023,2024,2026,2028,2032,2033,2887,2889,2891,2909,2910,2911,2913,2915,2925,2926,2927,2929,2931,2935,2936,2937,2939,2941,2952,2953,2954,2956,2958,2969,2970,2971,2973,2975,2988,2989,2990,2992,2994,2998,2999 TYPE the manner in which RMSD alignment is performed=DRMSD
alpha_ltThe LESS_THAN action with label alpha_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_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 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}
alphaThe SUM action with label alpha calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha
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_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Define the area you want to analyse
Protein_COMThe COM action with label Protein_COM calculates the following quantities:
 Quantity   
 Type   
 Description  
Protein_COM
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1145-3076 # not used, DBD plus part of core
DNA_centerThe COM action with label DNA_center calculates the following quantities:
 Quantity   
 Type   
 Description  
DNA_center
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe 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
hingeAThe COM action with label hingeA calculates the following quantities:
 Quantity   
 Type   
 Description  
hingeA
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe 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)
hingeBThe COM action with label hingeB calculates the following quantities:
 Quantity   
 Type   
 Description  
hingeB
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe 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)
distAThe DISTANCE action with label distA calculates the following quantities:
 Quantity   
 Type   
 Description  
distA
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=hingeA,DNA_center
distBThe DISTANCE action with label distB calculates the following quantities:
 Quantity   
 Type   
 Description  
distB
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=hingeB,DNA_center
distHThe DISTANCE action with label distH calculates the following quantities:
 Quantity   
 Type   
 Description  
distH
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=hingeA,hingeB

# define the DNA bending vector
p1_lThe COM action with label p1_l calculates the following quantities:
 Quantity   
 Type   
 Description  
p1_l
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-28,1111-1144 # first (fourth) bp
p1_rThe COM action with label p1_r calculates the following quantities:
 Quantity   
 Type   
 Description  
p1_r
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=539-600 # last (21st) bp
DNA_bentThe ANGLE action with label DNA_bent calculates the following quantities:
 Quantity   
 Type   
 Description  
DNA_bent
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)=p1_l,DNA_center,p1_r

# check for native contacts
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1239,938 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.5230 }
ATOMS2the atoms involved in each of the contacts you wish to calculate=1262,906 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4182 }
ATOMS3the atoms involved in each of the contacts you wish to calculate=1401,904 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3135 }
ATOMS4the atoms involved in each of the contacts you wish to calculate=1420,176 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2687 }
ATOMS5the atoms involved in each of the contacts you wish to calculate=1463,938 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4656 }
ATOMS6the atoms involved in each of the contacts you wish to calculate=1486,115 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3112 }
ATOMS7the atoms involved in each of the contacts you wish to calculate=1592,77 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4396 }
ATOMS8the atoms involved in each of the contacts you wish to calculate=2200,332 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4943 }
ATOMS9the atoms involved in each of the contacts you wish to calculate=2228,334 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3835 }
ATOMS10the atoms involved in each of the contacts you wish to calculate=2369,366 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2899 }
ATOMS11the atoms involved in each of the contacts you wish to calculate=2387,402 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2666 }
ATOMS12the atoms involved in each of the contacts you wish to calculate=2429,366 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4717 }
ATOMS13the atoms involved in each of the contacts you wish to calculate=2452,687 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2917 }
ATOMS14the atoms involved in each of the contacts you wish to calculate=2545,614 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4913 }
ATOMS15the atoms involved in each of the contacts you wish to calculate=1944,2917 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.5311 }
ATOMS16the atoms involved in each of the contacts you wish to calculate=1960,2917 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3087 }
ATOMS17the atoms involved in each of the contacts you wish to calculate=1965,2980 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3807 }
ATOMS18the atoms involved in each of the contacts you wish to calculate=1986,2917 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.6346 }
ATOMS19the atoms involved in each of the contacts you wish to calculate=1999,2921 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3000 }
ATOMS20the atoms involved in each of the contacts you wish to calculate=2018,2984 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3287 }
ATOMS21the atoms involved in each of the contacts you wish to calculate=2024,2984 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.6335 }
LABELa label for the action so that its output can be referenced in the input to other actions=cmapThe CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap
scalar
the sum of all the switching function on all the distances
SUM calculate the sum of all the contacts in the input
... CONTACTMAP

# check for native contacts, hinge
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1944,2917 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.5311 }
ATOMS2the atoms involved in each of the contacts you wish to calculate=1960,2917 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3087 }
ATOMS3the atoms involved in each of the contacts you wish to calculate=1965,2980 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3807 }
ATOMS4the atoms involved in each of the contacts you wish to calculate=1986,2917 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.6346 }
ATOMS5the atoms involved in each of the contacts you wish to calculate=1999,2921 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3000 }
ATOMS6the atoms involved in each of the contacts you wish to calculate=2018,2984 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3287 }
ATOMS7the atoms involved in each of the contacts you wish to calculate=2024,2984 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.6335 }
LABELa label for the action so that its output can be referenced in the input to other actions=cmap_hingeThe CONTACTMAP action with label cmap_hinge calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap_hinge
scalar
the sum of all the switching function on all the distances
SUM calculate the sum of all the contacts in the input
... CONTACTMAP

# check for native contacts, DNA
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1239,938 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.5230 }
ATOMS2the atoms involved in each of the contacts you wish to calculate=1262,906 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4182 }
ATOMS3the atoms involved in each of the contacts you wish to calculate=1401,904 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3135 }
ATOMS4the atoms involved in each of the contacts you wish to calculate=1420,176 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2687 }
ATOMS5the atoms involved in each of the contacts you wish to calculate=1463,938 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4656 }
ATOMS6the atoms involved in each of the contacts you wish to calculate=1486,115 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3112 }
ATOMS7the atoms involved in each of the contacts you wish to calculate=1592,77 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4396 }
ATOMS8the atoms involved in each of the contacts you wish to calculate=2200,332 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4943 }
ATOMS9the atoms involved in each of the contacts you wish to calculate=2228,334 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.3835 }
ATOMS10the atoms involved in each of the contacts you wish to calculate=2369,366 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2899 }
ATOMS11the atoms involved in each of the contacts you wish to calculate=2387,402 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2666 }
ATOMS12the atoms involved in each of the contacts you wish to calculate=2429,366 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4717 }
ATOMS13the atoms involved in each of the contacts you wish to calculate=2452,687 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.2917 }
ATOMS14the atoms involved in each of the contacts you wish to calculate=2545,614 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.4913 }
LABELa label for the action so that its output can be referenced in the input to other actions=cmap_DNAThe CONTACTMAP action with label cmap_DNA calculates the following quantities:
 Quantity   
 Type   
 Description  
cmap_DNA
scalar
the sum of all the switching function on all the distances
SUM calculate the sum of all the contacts in the input
... CONTACTMAP
# Print both collective variables on CVs file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cmap,alpha,DNA_bent,distH,distA,distB,cmap_DNA,cmap_hinge FILEthe name of the file on which to output these quantities=CVs STRIDE the frequency with which the quantities of interest should be output=1