Project ID: plumID:20.000
Source: funnel_metad/funnel_metad_plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# # This is the input file needed to perform funnel metadynamics simulation # based on the MC-HLDA CVs # # This input file can be used with all the PLUMED versions >=2.3 #
# Definition of the center of mass of the ligand, considering only its heavy atomsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1,5,6,10,14,17,18,19,22,23,24,25,26,29the list of atoms which are involved the virtual atom's definitionLABEL=ixoa label for the action so that its output can be referenced in the input to other actions
# Definition of the center of mass of the pocketCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1396,1398,1400,1403,1404,1406,1408,1409,1411,1413,1415,1416,1449,1451,1453,1456,1458,1459,1495,1497,1499,1501,1505,1509,1510,2838,2840,2842,2845,2846,2848,2850,2852,2854,2856,2857,3605,3607,3609,3612,3613,3615,3617,3618,3620,3622,3624,3625the list of atoms which are involved the virtual atom's definitionLABEL=pkta label for the action so that its output can be referenced in the input to other actions
# Definition of the distance between the ligand and the pocket as a 3d vector xyz # (the membrane is in the plane xy)DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=ixo,pktthe pair of atom that we are calculating the distance betweenLABEL=d1a label for the action so that its output can be referenced in the input to other actionsCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distances
# Definition of the periodicity of the components of the distance # (to avoid jumps in the variable during the simulation due to the # rototranslation of the system) d1x:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1.xthe input to this functionPERIODIC=-4.7,4.7 d1y:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1.ythe input to this functionPERIODIC=-4.7,4.7 d1z:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1.zthe input to this functionPERIODIC=-8.2,8.2if the output of your function is periodic then you should specify the periodicity of the function
# We define the radius of the funnel potential on the xy plane (the same of the membrane) radius:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=d1x,d1ythe input to this functionVAR=x,ythe names to give each of the arguments in the functionFUNC=sqrt(x*x+y*ythe function you wish to evaluatePERIODIC=NO # We define the conical and the cylindrical part of the funnel potential funnel:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=radius,d1zthe input to this functionVAR=r,zthe names to give each of the arguments in the functionFUNC=(r-(z+1.8))*step(z+1.7)+(r-0.1)*step(-1.7-zthe function you wish to evaluatePERIODIC=NO # We define the funnel potentialif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=0the positions of the wallARG=funnelthe arguments on which the bias is actingKAPPA=2000.0the force constant for the wallLABEL=funnelwalla label for the action so that its output can be referenced in the input to other actions
# Wall on distance to prevent the ligand exit to the solventLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=-4.0the positions of the wallARG=d1.zthe arguments on which the bias is actingKAPPA=2000.0the force constant for the wallLABEL=topwall # Wall on distance to prevent the ligand entering the intracellular parta label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=0.3the positions of the wallARG=d1.zthe arguments on which the bias is actingKAPPA=2000.0the force constant for the wallLABEL=bottomwalla label for the action so that its output can be referenced in the input to other actions
# Contact related to the nonbonded interactions in bound state bound_d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=25,3637 bound_d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,3637 bound_d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=25,2842 bound_d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=26,2837 bound_d5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,3620 bound_d6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=26,1505 bound_d7:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=17,1398the pair of atom that we are calculating the distance between
# Contact related to the nonbonded interactions in state A cl2_d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=25,1409 cl2_d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,1409 cl2_d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,1456 cl2_d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,1411 cl2_d5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=19,3622 cl2_d6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,1408the pair of atom that we are calculating the distance between
# Contact related to the nonbonded interactions in state B cl3_d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,1404 cl3_d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,3975 cl3_d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,1413 cl3_d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,3613the pair of atom that we are calculating the distance between
# Contact related to the nonbonded interactions in state C cl5_d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,3618 cl5_d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=25,3618 cl5_d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=23,3615 cl5_d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=29,2791the pair of atom that we are calculating the distance between
# Salt bridges sb_d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,1392 sb_d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,1393the pair of atom that we are calculating the distance between
# Eigenvectors from the MC-HLDA analysis on the contacts eig1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2the input to this functionCOEFFICIENTS=0.312,-0.262,0.116,0.021,0.411,0.020,0.073,0.484,-0.490,0.004,0.007,-0.008,-0.002,-0.037,-0.009,-0.001,0.085,-0.054,-0.347,-0.153,0.124,-0.022,-0.012the coefficients of the arguments in your functionPERIODIC=NO eig2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2the input to this functionCOEFFICIENTS=-0.509,0.468,0.025,0.031,-0.211,-0.003,-0.008,0.239,-0.218,-0.002,-0.004,-0.227,-0.019,0.005,0.006,-0.006,-0.173,0.106,0.430,0.090,0.289,0.015,0.029the coefficients of the arguments in your functionPERIODIC=NO eig3:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2the input to this functionCOEFFICIENTS=-0.367,0.354,-0.078,-0.003,0.104,-0.008,-0.118,0.424,-0.307,-0.011,0.063,0.077,-0.059,0.119,0.014,0.004,0.175,-0.558,0.237,0.089,0.013,0.021,0.022the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Multiple-walkers well-tempered metadynamics on the MC-HLDA eigenvectorsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=eig1,eig2the input for this action is the scalar output from one or more other actionsPACE=500the frequency for hill additionHEIGHT=1.2the heights of the Gaussian hillsBIASFACTOR=24use well tempered metadynamics and use this bias factorTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.015,0.015the widths of the Gaussian hillsFILE=../HILLSa file in which the list of added hills is storedGRID_MIN=-0.1,-0.2the lower bounds for the gridGRID_MAX=2.,2the upper bounds for the gridWALKERS_MPI... METADSwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
# Here we print all the data regarding metadynamicsPrint quantities to a file. More detailsARG=metadthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=metaD_data # Here we print all the data regarding barriersthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=d1.z,topwall.*,bottomwallthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=IXO_dist.dat # Here we print all the data regarding ligand position and funnel potentialthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=d1.x,d1.y,d1.z,d1x,d1y,d1z,radius,funnel,funnelwallthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=funnel_dist.dat # Here we print all the data regarding the MC-HLDA eigenvectorsthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=eig1,eig2,eig3the input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=eigenvectors.dat # Here we print all the distances for the contactsthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2the input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=contacts.datthe name of the file on which to output these quantitiesENDPLUMEDTerminate plumed input. More details