PLUMED-NEST-TEST-SITE

Project ID: plumID:23.006
Source: PLUMED_input/PLUMED_files/OSymL/DNA_bending/plumed_run.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_noTet_99sbws_proc_mod_resID.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=10520-10522,10550-10552,11281-11283,11311-11313 # P and OP of central two basepairs
# DNA_p2: COM ATOMS=10613-10624,11216-11227 #not used, point on the DNA
# 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

# 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=10261-10291,11562-11593
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=10801-10832,11022-11053
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=82,10596 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=0.5214 }
ATOMS2the atoms involved in each of the contacts you wish to calculate=101,10601 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=0.3574 }
ATOMS3the atoms involved in each of the contacts you wish to calculate=240,11198 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=0.3145 }
ATOMS4the atoms involved in each of the contacts you wish to calculate=260,10663 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=0.2724 }
ATOMS5the atoms involved in each of the contacts you wish to calculate=302,10626 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=0.4654 }
ATOMS6the atoms involved in each of the contacts you wish to calculate=325,11136 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=0.2997 }
ATOMS7the atoms involved in each of the contacts you wish to calculate=418,11069 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=0.4366 }
ATOMS8the atoms involved in each of the contacts you wish to calculate=5167,11357 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=0.4923 }
ATOMS9the atoms involved in each of the contacts you wish to calculate=5186,11362 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=0.3194 }
ATOMS10the atoms involved in each of the contacts you wish to calculate=5325,10440 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=0.2879 }
ATOMS11the atoms involved in each of the contacts you wish to calculate=5345,11424 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=0.2696 }
ATOMS12the atoms involved in each of the contacts you wish to calculate=5387,11389 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=0.4696 }
ATOMS13the atoms involved in each of the contacts you wish to calculate=5410,10372 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=0.2914 }
ATOMS14the atoms involved in each of the contacts you wish to calculate=5516,10340 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=0.4955 }
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

# Activate well-tempered metadynamics in alpharmsd, cmap (specific contacts and hinge contacts) and DNA bending
   # Deposit a Gaussian every 100 time steps, with initial height 
   # equal to 1.3 kJ/mol and bias factor equal to 10 
   # Gaussian width (sigma) is determined with the adaptive sheme to correspond to 0.25 nm with a minimum width of 0.05 CV units 
   # Gaussians will be written to file and also stored on grid
#
metaDThe METAD action with label metaD calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD.bias
scalar
the instantaneous value of the bias potential
metaD.acc
scalar
the metadynamics acceleration factor: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cmap,alpha,DNA_bent ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM SIGMAthe widths of the Gaussian hills=0.25 PACEthe frequency for hill addition=100 HEIGHTthe heights of the Gaussian hills=1.3 BIASFACTORuse well tempered metadynamics and use this bias factor=10 FILE a file in which the list of added hills is stored=HILLS ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor GRID_MINthe lower bounds for the grid=0,0,0 GRID_MAXthe upper bounds for the grid=21,4,3.1416 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.02,0.02,0.02 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.05,0.05,0.05 
# Print both collective variables on COLVAR file every 10 steps
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=alpha,cmap,metaD.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=10
# Print both collective variables on COLVAR file every 10 steps
# Dump the forces and print to file
DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=cmap,alpha,DNA_bent STRIDE the frequency with which the forces should be output=10 FILEthe name of the file on which to output the forces=forces