PLUMED-NEST-TEST-SITE

Project ID: plumID:23.006
Source: 1OSL_CV_analsyis/plumed_print_1efa.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 somethingalpha: ALPHARMSDProbe the alpha helical content of a protein structure. 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   
# Define the area you want to analyse
The ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Description  
alpha.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
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: 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
The COM action with label Protein_COM calculates somethingDNA_center: 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
# DNA_p2: COM ATOMS=10613-10624,11216-11227
# Define the distance between the hinges and the DNA center
The COM action with label DNA_center calculates somethinghingeA: 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
The COM action with label hingeA calculates somethinghingeB: 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
The COM action with label hingeB calculates somethingdistA: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=hingeA,DNA_center
The DISTANCE action with label distA calculates the following quantities:
 Quantity   
 Description  
distA.value
the DISTANCE between this pair of atomsdistB: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=hingeB,DNA_center
The DISTANCE action with label distB calculates the following quantities:
 Quantity   
 Description  
distB.value
the DISTANCE between this pair of atomsdistH: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=hingeA,hingeB 
# check for native contacts
The DISTANCE action with label distH calculates the following quantities:
 Quantity   
 Description  
distH.value
the DISTANCE between this pair of atomsCONTACTMAPCalculate 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=cmap
SUM calculate the sum of all the contacts in the input
... CONTACTMAP

# check for native contacts, protein
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
cmap.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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_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
cmap_hinge.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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 }
LABELa 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 all the contacts and check them
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
cmap_DNA.value
the sum of all the switching function on all the distancesdist1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=82,10596 
The DISTANCE action with label dist1 calculates the following quantities:
 Quantity   
 Description  
dist1.value
the DISTANCE between this pair of atomsdist2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,10601 
The DISTANCE action with label dist2 calculates the following quantities:
 Quantity   
 Description  
dist2.value
the DISTANCE between this pair of atomsdist3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=240,11198 
The DISTANCE action with label dist3 calculates the following quantities:
 Quantity   
 Description  
dist3.value
the DISTANCE between this pair of atomsdist4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=260,10663
The DISTANCE action with label dist4 calculates the following quantities:
 Quantity   
 Description  
dist4.value
the DISTANCE between this pair of atomsdist5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=302,10626 
The DISTANCE action with label dist5 calculates the following quantities:
 Quantity   
 Description  
dist5.value
the DISTANCE between this pair of atomsdist6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=325,11136
The DISTANCE action with label dist6 calculates the following quantities:
 Quantity   
 Description  
dist6.value
the DISTANCE between this pair of atomsdist7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=418,11069
The DISTANCE action with label dist7 calculates the following quantities:
 Quantity   
 Description  
dist7.value
the DISTANCE between this pair of atomsdist8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5167,11357
The DISTANCE action with label dist8 calculates the following quantities:
 Quantity   
 Description  
dist8.value
the DISTANCE between this pair of atomsdist9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5186,11362  
The DISTANCE action with label dist9 calculates the following quantities:
 Quantity   
 Description  
dist9.value
the DISTANCE between this pair of atomsdist10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5325,10440 
The DISTANCE action with label dist10 calculates the following quantities:
 Quantity   
 Description  
dist10.value
the DISTANCE between this pair of atomsdist11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5345,11424
The DISTANCE action with label dist11 calculates the following quantities:
 Quantity   
 Description  
dist11.value
the DISTANCE between this pair of atomsdist12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5387,11389 
The DISTANCE action with label dist12 calculates the following quantities:
 Quantity   
 Description  
dist12.value
the DISTANCE between this pair of atomsdist13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5410,10372 
The DISTANCE action with label dist13 calculates the following quantities:
 Quantity   
 Description  
dist13.value
the DISTANCE between this pair of atomsdist14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5516,10340 
The DISTANCE action with label dist14 calculates the following quantities:
 Quantity   
 Description  
dist14.value
the DISTANCE between this pair of atomsdist15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=783,5875
The DISTANCE action with label dist15 calculates the following quantities:
 Quantity   
 Description  
dist15.value
the DISTANCE between this pair of atomsdist16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=799,5875 
The DISTANCE action with label dist16 calculates the following quantities:
 Quantity   
 Description  
dist16.value
the DISTANCE between this pair of atomsdist17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=804,5938 
The DISTANCE action with label dist17 calculates the following quantities:
 Quantity   
 Description  
dist17.value
the DISTANCE between this pair of atomsdist18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=825,5875 
The DISTANCE action with label dist18 calculates the following quantities:
 Quantity   
 Description  
dist18.value
the DISTANCE between this pair of atomsdist19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=838,5879 
The DISTANCE action with label dist19 calculates the following quantities:
 Quantity   
 Description  
dist19.value
the DISTANCE between this pair of atomsdist20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=857,5942 
The DISTANCE action with label dist20 calculates the following quantities:
 Quantity   
 Description  
dist20.value
the DISTANCE between this pair of atomsdist21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=863,5942 

# define the DNA bending vector
The DISTANCE action with label dist21 calculates the following quantities:
 Quantity   
 Description  
dist21.value
the DISTANCE between this pair of atomsp1_l: 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
The COM action with label p1_l calculates somethingp1_r: 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
The COM action with label p1_r calculates somethingDNA_bent: 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

# this is printing the electrostatic interaction between protein and DNA
# dh: DHENERGY GROUPA=1- GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=310.0  
# Print both collective variables on CVs file
The ANGLE action with label DNA_bent calculates the following quantities:
 Quantity   
 Description  
DNA_bent.value
the ANGLE involving these atomsPRINTPrint 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