PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:23.006
Source: PLUMED_input/PLUMED_files/NOD/alphaRMSD/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=1efa_NOD_S99_mod_ID.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=50-56,385-391   
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=50-56,385-391  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=50-56,385-391   
# 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=760,762,764,782,783,784,786,788,798,799,800,802,804,808,809,810,812,814,825,826,827,829,831,842,843,844,846,848,861,862,863,865,867,871,872,5845,5847,5849,5867,5868,5869,5871,5873,5883,5884,5885,5887,5889,5893,5894,5895,5897,5899,5910,5911,5912,5914,5916,5927,5928,5929,5931,5933,5946,5947,5948,5950,5952,5956,5957 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=1-1648,5086-6733 # 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=10520-10522,10553-10555,11284-11286,11316-11318 # 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=760,762,782-784,786,799-800,802,808-810,812,825-827,829,842-844,846,861-863,865,878-879 # 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=5845,5847,5867-5869,5871,5883-5885,5887,5893-5895,5897,5910-5912,5914,5927-5929,5931,5946-5948,5950,5956-5957 # 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=10262-10294,11568-11597
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=10807-10839,11029-11058
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=82,10598 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=101,10603 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=240,11203 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=260,10670 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=302,10630 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=325,11106 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=418,11074 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=5167,11359 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=5186,11361 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=5325,10442 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=5345,11431 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=5387,11391 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=5410,10374 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=5516,10342 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=783,5875 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=799,5875 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=804,5938 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=825,5875 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=838,5879 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=857,5942 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=863,5942 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=783,5875 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=799,5875 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=804,5938 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=825,5875 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=838,5879 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=857,5942 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=863,5942 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=82,10598 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=101,10603 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=240,11203 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=260,10670 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=302,10630 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=325,11106 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=418,11074 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=5167,11359 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=5186,11361 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=5325,10442 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=5345,11431 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=5387,11391 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=5410,10374 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=5516,10342 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 all the contacts and check them
dist1The DISTANCE action with label dist1 calculates the following quantities: Quantity    Type    Description  
dist1 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=82,10598 
dist2The DISTANCE action with label dist2 calculates the following quantities: Quantity    Type    Description  
dist2 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=101,10603 
dist3The DISTANCE action with label dist3 calculates the following quantities: Quantity    Type    Description  
dist3 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=240,11203 
dist4The DISTANCE action with label dist4 calculates the following quantities: Quantity    Type    Description  
dist4 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=260,10670
dist5The DISTANCE action with label dist5 calculates the following quantities: Quantity    Type    Description  
dist5 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=302,10630 
dist6The DISTANCE action with label dist6 calculates the following quantities: Quantity    Type    Description  
dist6 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=325,11106
dist7The DISTANCE action with label dist7 calculates the following quantities: Quantity    Type    Description  
dist7 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=418,11074
dist8The DISTANCE action with label dist8 calculates the following quantities: Quantity    Type    Description  
dist8 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=5167,11359
dist9The DISTANCE action with label dist9 calculates the following quantities: Quantity    Type    Description  
dist9 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=5186,11361  
dist10The DISTANCE action with label dist10 calculates the following quantities: Quantity    Type    Description  
dist10 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=5325,10442 
dist11The DISTANCE action with label dist11 calculates the following quantities: Quantity    Type    Description  
dist11 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=5345,11431
dist12The DISTANCE action with label dist12 calculates the following quantities: Quantity    Type    Description  
dist12 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=5387,11391 
dist13The DISTANCE action with label dist13 calculates the following quantities: Quantity    Type    Description  
dist13 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=5410,10374 
dist14The DISTANCE action with label dist14 calculates the following quantities: Quantity    Type    Description  
dist14 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=5516,10342 
dist15The DISTANCE action with label dist15 calculates the following quantities: Quantity    Type    Description  
dist15 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=783,5875
dist16The DISTANCE action with label dist16 calculates the following quantities: Quantity    Type    Description  
dist16 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=799,5875  
dist17The DISTANCE action with label dist17 calculates the following quantities: Quantity    Type    Description  
dist17 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=804,5938 
dist18The DISTANCE action with label dist18 calculates the following quantities: Quantity    Type    Description  
dist18 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=825,5875
dist19The DISTANCE action with label dist19 calculates the following quantities: Quantity    Type    Description  
dist19 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=838,5879 
dist20The DISTANCE action with label dist20 calculates the following quantities: Quantity    Type    Description  
dist20 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=857,5942 
dist21The DISTANCE action with label dist21 calculates the following quantities: Quantity    Type    Description  
dist21 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=863,5942 


# 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
#Print individual distances to distance file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dist1,dist2,dist3,dist4,dist5,dist6,dist7,dist8,dist9,dist10,dist11,dist12,dist13,dist14,dist15,dist16,dist17,dist18,dist19,dist20,dist21 FILEthe name of the file on which to output these quantities=distances STRIDE the frequency with which the quantities of interest should be output=1
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
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
