Project ID: plumID:23.006
Source: PLUMED_input/PLUMED_files/OSymL/DNA_bending/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
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# Activate MOLINFO functionalitiesMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=1efa_noTet_99sbws_proc_mod_resID.pdba file in pdb format containing a reference structureMOLTYPE=protein # alphaRMSD alpha:what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleALPHARMSDProbe the alpha helical content of a protein structure. More detailsRESIDUES=50-56,385-391 # Define the area you want to analyse Protein_COM:this command is used to specify the set of residues that could conceivably form part of the secondary structureCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-1648,5086-6733 # not used, DBD plus part of core DNA_center:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=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 hingeA:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=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) hingeB:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=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) distA:the list of atoms which are involved the virtual atom's definitionDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=hingeA,DNA_center distB:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=hingeB,DNA_center distH:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=hingeA,hingeB # define the DNA bending vector p1_l:the pair of atom that we are calculating the distance betweenCOMCalculate the center of mass for a group of atoms. More detailsATOMS=10261-10291,11562-11593 p1_r:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=10801-10832,11022-11053 DNA_bent:the list of atoms which are involved the virtual atom's definitionANGLECalculate an angle. More detailsATOMS=p1_l,DNA_center,p1_rthe list of atoms involved in this collective variable (either 3 or 4 atoms)
# check for native contactsCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=82,10596the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.3 D_0=0.5214 }The switching functions to use for each of the contacts in your mapATOMS2=101,10601the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.3 D_0=0.3574 }The switching functions to use for each of the contacts in your mapATOMS3=240,11198the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.3 D_0=0.3145 }The switching functions to use for each of the contacts in your mapATOMS4=260,10663the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.3 D_0=0.2724 }The switching functions to use for each of the contacts in your mapATOMS5=302,10626the atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=0.3 D_0=0.4654 }The switching functions to use for each of the contacts in your mapATOMS6=325,11136the atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=0.3 D_0=0.2997 }The switching functions to use for each of the contacts in your mapATOMS7=418,11069the atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=0.3 D_0=0.4366 }The switching functions to use for each of the contacts in your mapATOMS8=5167,11357the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=0.3 D_0=0.4923 }The switching functions to use for each of the contacts in your mapATOMS9=5186,11362the atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.3 D_0=0.3194 }The switching functions to use for each of the contacts in your mapATOMS10=5325,10440the atoms involved in each of the contacts you wish to calculateSWITCH10={RATIONAL R_0=0.3 D_0=0.2879 }The switching functions to use for each of the contacts in your mapATOMS11=5345,11424the atoms involved in each of the contacts you wish to calculateSWITCH11={RATIONAL R_0=0.3 D_0=0.2696 }The switching functions to use for each of the contacts in your mapATOMS12=5387,11389the atoms involved in each of the contacts you wish to calculateSWITCH12={RATIONAL R_0=0.3 D_0=0.4696 }The switching functions to use for each of the contacts in your mapATOMS13=5410,10372the atoms involved in each of the contacts you wish to calculateSWITCH13={RATIONAL R_0=0.3 D_0=0.2914 }The switching functions to use for each of the contacts in your mapATOMS14=5516,10340the atoms involved in each of the contacts you wish to calculateSWITCH14={RATIONAL R_0=0.3 D_0=0.4955 }The switching functions to use for each of the contacts in your mapATOMS15=783,5875the atoms involved in each of the contacts you wish to calculateSWITCH15={RATIONAL R_0=0.3 D_0=0.5311 }The switching functions to use for each of the contacts in your mapATOMS16=799,5875the atoms involved in each of the contacts you wish to calculateSWITCH16={RATIONAL R_0=0.3 D_0=0.3087 }The switching functions to use for each of the contacts in your mapATOMS17=804,5938the atoms involved in each of the contacts you wish to calculateSWITCH17={RATIONAL R_0=0.3 D_0=0.3807 }The switching functions to use for each of the contacts in your mapATOMS18=825,5875the atoms involved in each of the contacts you wish to calculateSWITCH18={RATIONAL R_0=0.3 D_0=0.6346 }The switching functions to use for each of the contacts in your mapATOMS19=838,5879the atoms involved in each of the contacts you wish to calculateSWITCH19={RATIONAL R_0=0.3 D_0=0.3000 }The switching functions to use for each of the contacts in your mapATOMS20=857,5942the atoms involved in each of the contacts you wish to calculateSWITCH20={RATIONAL R_0=0.3 D_0=0.3287 }The switching functions to use for each of the contacts in your mapATOMS21=863,5942the atoms involved in each of the contacts you wish to calculateSWITCH21={RATIONAL R_0=0.3 D_0=0.6335 }The switching functions to use for each of the contacts in your mapLABEL=cmapa label for the action so that its output can be referenced in the input to other actionsSUM... CONTACTMAPcalculate the sum of all the contacts in the input
# check for native contacts, hingeCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=783,5875the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.3 D_0=0.5311 }The switching functions to use for each of the contacts in your mapATOMS2=799,5875the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.3 D_0=0.3087 }The switching functions to use for each of the contacts in your mapATOMS3=804,5938the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.3 D_0=0.3807 }The switching functions to use for each of the contacts in your mapATOMS4=825,5875the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.3 D_0=0.6346 }The switching functions to use for each of the contacts in your mapATOMS5=838,5879the atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=0.3 D_0=0.3000 }The switching functions to use for each of the contacts in your mapATOMS6=857,5942the atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=0.3 D_0=0.3287 }The switching functions to use for each of the contacts in your mapATOMS7=863,5942the atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=0.3 D_0=0.6335 }The switching functions to use for each of the contacts in your mapLABEL=cmap_hingea label for the action so that its output can be referenced in the input to other actionsSUM... CONTACTMAPcalculate the sum of all the contacts in the input
# check for native contacts, DNACONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=82,10596the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.3 D_0=0.5214 }The switching functions to use for each of the contacts in your mapATOMS2=101,10601the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.3 D_0=0.3574 }The switching functions to use for each of the contacts in your mapATOMS3=240,11198the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.3 D_0=0.3145 }The switching functions to use for each of the contacts in your mapATOMS4=260,10663the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.3 D_0=0.2724 }The switching functions to use for each of the contacts in your mapATOMS5=302,10626the atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=0.3 D_0=0.4654 }The switching functions to use for each of the contacts in your mapATOMS6=325,11136the atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=0.3 D_0=0.2997 }The switching functions to use for each of the contacts in your mapATOMS7=418,11069the atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=0.3 D_0=0.4366 }The switching functions to use for each of the contacts in your mapATOMS8=5167,11357the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=0.3 D_0=0.4923 }The switching functions to use for each of the contacts in your mapATOMS9=5186,11362the atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.3 D_0=0.3194 }The switching functions to use for each of the contacts in your mapATOMS10=5325,10440the atoms involved in each of the contacts you wish to calculateSWITCH10={RATIONAL R_0=0.3 D_0=0.2879 }The switching functions to use for each of the contacts in your mapATOMS11=5345,11424the atoms involved in each of the contacts you wish to calculateSWITCH11={RATIONAL R_0=0.3 D_0=0.2696 }The switching functions to use for each of the contacts in your mapATOMS12=5387,11389the atoms involved in each of the contacts you wish to calculateSWITCH12={RATIONAL R_0=0.3 D_0=0.4696 }The switching functions to use for each of the contacts in your mapATOMS13=5410,10372the atoms involved in each of the contacts you wish to calculateSWITCH13={RATIONAL R_0=0.3 D_0=0.2914 }The switching functions to use for each of the contacts in your mapATOMS14=5516,10340the atoms involved in each of the contacts you wish to calculateSWITCH14={RATIONAL R_0=0.3 D_0=0.4955 }The switching functions to use for each of the contacts in your mapLABEL=cmap_DNAa label for the action so that its output can be referenced in the input to other actionsSUM... CONTACTMAP # Print all the contacts and check them dist1:calculate the sum of all the contacts in the inputDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=82,10596 dist2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=101,10601 dist3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=240,11198 dist4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=260,10663 dist5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=302,10626 dist6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=325,11136 dist7:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=418,11069 dist8:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5167,11357 dist9:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5186,11362 dist10:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5325,10440 dist11:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5345,11424 dist12:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5387,11389 dist13:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5410,10372 dist14:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5516,10340 dist15:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=783,5875 dist16:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=799,5875 dist17:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=804,5938 dist18:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=825,5875 dist19:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=838,5879 dist20:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=857,5942 dist21:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=863,5942the pair of atom that we are calculating the distance between
# Print all collective variables on CVs filePrint quantities to a file. More detailsARG=cmap,alpha,DNA_bent,distH,distA,distB,cmap_DNA,cmap_hingethe input for this action is the scalar output from one or more other actionsFILE=CVsthe name of the file on which to output these quantitiesSTRIDE=1 #Print individual distances to distance filethe frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=dist1,dist2,dist3,dist4,dist5,dist6,dist7,dist8,dist9,dist10,dist11,dist12,dist13,dist14,dist15,dist16,dist17,dist18,dist19,dist20,dist21the input for this action is the scalar output from one or more other actionsFILE=distancesthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output