Project ID: plumID:23.006
Source: PLUMED_input/PLUMED_files/OSymL/hinge_contacts/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
# 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_centerthe pair of atom that we are calculating the distance between
# 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
# Activate well-tempered metadynamics in cmap (specific contacts) # 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 # metaD:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=cmapthe input for this action is the scalar output from one or more other actionsADAPTIVE=GEOMuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA=0.25the widths of the Gaussian hillsPACE=100the frequency for hill additionHEIGHT=1.3the heights of the Gaussian hillsBIASFACTOR=10use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is storedACCELERATIONSet to TRUE if you want to compute the metadynamics acceleration factorGRID_MIN=0the lower bounds for the gridGRID_MAX=21the upper bounds for the gridGRID_SPACING=0.02the approximate grid spacing (to be used as an alternative or together with GRID_BIN)SIGMA_MIN=0.05 # Print both collective variables on COLVAR file every 10 stepsthe lower bounds for the sigmas (in CV units) when using adaptive hillsPrint quantities to a file. More detailsARG=alpha,cmap,metaDthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=10 # Print both collective variables on COLVAR file every 10 steps # Dump the forces and print to filethe frequency with which the quantities of interest should be outputDUMPFORCESDump the force acting on one of a values in a file. More detailsARG=cmap,alphathe input for this action is the scalar output from one or more other actionsSTRIDE=10the frequency with which the forces should be outputFILE=forcesthe name of the file on which to output the forces