Project ID: plumID:23.006
Source: PLUMED_input/PLUMED_files/NOD/alphaRMSD/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
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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_NOD_S99_mod_ID.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=10520-10522,10553-10555,11284-11286,11316-11318 # P and OP of central two basepairsthe list of atoms which are involved the virtual atom's definition
# Define the distance between the hinges and the DNA center hingeA:COMCalculate 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=82,10598the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.3 D_0=0.5230 }The switching functions to use for each of the contacts in your mapATOMS2=101,10603the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.3 D_0=0.4182 }The switching functions to use for each of the contacts in your mapATOMS3=240,11203the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.3 D_0=0.3135 }The switching functions to use for each of the contacts in your mapATOMS4=260,10670the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.3 D_0=0.2687 }The switching functions to use for each of the contacts in your mapATOMS5=302,10630the atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=0.3 D_0=0.4656 }The switching functions to use for each of the contacts in your mapATOMS6=325,11106the atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=0.3 D_0=0.3112 }The switching functions to use for each of the contacts in your mapATOMS7=418,11074the atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=0.3 D_0=0.4396 }The switching functions to use for each of the contacts in your mapATOMS8=5167,11359the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=0.3 D_0=0.4943 }The switching functions to use for each of the contacts in your mapATOMS9=5186,11361the atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.3 D_0=0.3835 }The switching functions to use for each of the contacts in your mapATOMS10=5325,10442the atoms involved in each of the contacts you wish to calculateSWITCH10={RATIONAL R_0=0.3 D_0=0.2899 }The switching functions to use for each of the contacts in your mapATOMS11=5345,11431the atoms involved in each of the contacts you wish to calculateSWITCH11={RATIONAL R_0=0.3 D_0=0.2666 }The switching functions to use for each of the contacts in your mapATOMS12=5387,11391the atoms involved in each of the contacts you wish to calculateSWITCH12={RATIONAL R_0=0.3 D_0=0.4717 }The switching functions to use for each of the contacts in your mapATOMS13=5410,10374the atoms involved in each of the contacts you wish to calculateSWITCH13={RATIONAL R_0=0.3 D_0=0.2917 }The switching functions to use for each of the contacts in your mapATOMS14=5516,10342the atoms involved in each of the contacts you wish to calculateSWITCH14={RATIONAL R_0=0.3 D_0=0.4913 }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 alpharmsd and 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=cmap,alphathe 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=0,0the lower bounds for the gridGRID_MAX=21,4the upper bounds for the gridGRID_SPACING=0.02,0.02the approximate grid spacing (to be used as an alternative or together with GRID_BIN)SIGMA_MIN=0.05,0.05 # 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