Project ID: plumID:20.005
Source: input_data/classical/FA-metaD/FA-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
Click on the labels of the actions for more information on what each action computes
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# # This is the input file needed to perform Multiple # Walkers WT-MetaD simulation based on the pathCV # # This input file can be used with all the PLUMED versions >=2.5 #MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../input_files/first.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-6250the atoms that make up a molecule that you wish to align
# 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 actionsDISTANCECalculate 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
# Restraining potential of the ligandDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=ixo,pktthe pair of atom that we are calculating the distance betweenLABEL=restra label for the action so that its output can be referenced in the input to other actionsNOPBCsphere:ignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=restrthe arguments on which the bias is actingAT=2.5the positions of the wallKAPPA=1000the force constant for the wall
#ligand ring:COMCalculate the center of mass for a group of atoms. More detailsATOMS=23,24,25,26,29 #ixo: COM ATOMS=1,5,6,10,14,17,18,19,22,23,24,25,26,29the list of atoms which are involved the virtual atom's definition
# Trimetylammonium interactions ring244:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3971,3972,3974,3976,3979,3981 ring221:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3614,3615,3617,3619,3622,3624 ring86:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1405,1406,1408,1410,1413,1415 oxy85:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1394,1395the list of atoms which are involved the virtual atom's definition
# Ligand ring interactions val93:COMCalculate the center of mass for a group of atoms. More detailsATOMS=1501,1503,1507 ile160:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=2605,2609,2612 thr169:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=2740,2742,2746the list of atoms which are involved the virtual atom's definition
# all ligand interactions trp218:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3566,3567,3569,3571,3572,3574,3576,3578,3580 cys158:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=2572,2575the list of atoms which are involved the virtual atom's definition
# Definition of the contact maps for the pathCVCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.324857000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.326715000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.317481000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.916788000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.988975000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.985199000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.459210000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.532785000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.151720000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm1a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.322060000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.322125000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.318081000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.940059000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.974572000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.912335000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.641878000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.522181000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.308574000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm2a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.320523000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.324186000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.315741000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.918387000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.782751000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.416873000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.918085000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.519385000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.736644000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm3a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.324818000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.316640000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.316240000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.922710000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.392776000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.178666000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.919086000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.532663000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.949034000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm4a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.326082000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.325629000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.303538000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.887596000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.143690000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.064591000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.999237000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.587326000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.878697000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm5a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.328269000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.327338000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.320984000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.914713000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.062782000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.033614000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.998120000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.734615000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.777428000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm6a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.326594000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.326341000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.321865000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.893738000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.049625000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.020003000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.996938000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.648535000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.469544000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm7a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.326402000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.324290000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.317068000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.765955000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.036467000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.015861000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.990764000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.636723000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.498470000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm8a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.216448000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.239333000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.182106000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.169182000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.008046000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.003324000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.674940000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.784664000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.083936000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm9a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.044800000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.032370000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.022490000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.041785000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.001275000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.000763000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.067223000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.764340000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.031289000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm10a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.010987000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.010682000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.007535000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.013361000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.000552000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.000381000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.024819000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.413170000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.018060000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm11a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=5,ring244the atoms involved in each of the contacts you wish to calculateSWITCH1={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE1=0.000000000A reference value for a given contact, by default is 0WEIGHT1=0.333A weight value for a given contact, by default is 1ATOMS2=5,ring221the atoms involved in each of the contacts you wish to calculateSWITCH2={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE2=0.000000000A reference value for a given contact, by default is 0WEIGHT2=0.333A weight value for a given contact, by default is 1ATOMS3=5,ring86the atoms involved in each of the contacts you wish to calculateSWITCH3={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE3=0.000000000A reference value for a given contact, by default is 0WEIGHT3=0.333A weight value for a given contact, by default is 1ATOMS4=5,oxy85the atoms involved in each of the contacts you wish to calculateSWITCH4={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE4=0.000000000A reference value for a given contact, by default is 0WEIGHT4=1A weight value for a given contact, by default is 1ATOMS5=trp218,ringthe atoms involved in each of the contacts you wish to calculateSWITCH5={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE5=0.000000000A reference value for a given contact, by default is 0WEIGHT5=1A weight value for a given contact, by default is 1ATOMS6=val93,ringthe atoms involved in each of the contacts you wish to calculateSWITCH6={RATIONAL R_0=1.0 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE6=0.000000000A reference value for a given contact, by default is 0WEIGHT6=1A weight value for a given contact, by default is 1ATOMS7=ile160,ringthe atoms involved in each of the contacts you wish to calculateSWITCH7={RATIONAL R_0=1.2 NN=6 MM=12}The switching functions to use for each of the contacts in your mapREFERENCE7=0.000000000A reference value for a given contact, by default is 0WEIGHT7=1A weight value for a given contact, by default is 1ATOMS8=5,cys158the atoms involved in each of the contacts you wish to calculateSWITCH8={RATIONAL R_0=1.2 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE8=0.000000000A reference value for a given contact, by default is 0WEIGHT8=1A weight value for a given contact, by default is 1ATOMS9=thr169,ringthe atoms involved in each of the contacts you wish to calculateSWITCH9={RATIONAL R_0=0.8 NN=6 MM=10}The switching functions to use for each of the contacts in your mapREFERENCE9=0.000000000A reference value for a given contact, by default is 0WEIGHT9=1A weight value for a given contact, by default is 1LABEL=cm12a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAP # Definition of the pathCV p1:calculate the distance with respect to the provided reference contact mapFUNCPATHMSDThis function calculates path collective variables. More detailsARG=cm1,cm2,cm3,cm4,cm5,cm6,cm7,cm8,cm9,cm10,cm11,cm12the input for this action is the scalar output from one or more other actionsLAMBDA=9.778314the lambda parameter is needed for smoothing, is in the units of plumed
# Restraining to maintain the ligand on the pathway I ort_up:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=p1.zthe arguments on which the bias is actingAT=0.23the positions of the wallKAPPA=50000 ort_down:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=p1.zthe arguments on which the bias is actingAT=-0.2the positions of the wallKAPPA=1000the force constant for the wall
# Frequency-Adaptive MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=p1.s,p1.zthe input for this action is the scalar output from one or more other actionsGRID_MIN=1.,-0.2the lower bounds for the gridGRID_MAX=12.,0.4the upper bounds for the gridHEIGHT=2the heights of the Gaussian hillsSIGMA=0.05,0.01the widths of the Gaussian hillsBIASFACTOR=20use well tempered metadynamics and use this bias factorLABEL=metada label for the action so that its output can be referenced in the input to other actionsTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]ACCELERATIONSet to TRUE if you want to compute the metadynamics acceleration factorFREQUENCY_ADAPTIVESet to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factorPACE=500the frequency for hill additionFA_MAX_PACE=50000the maximum hill addition frequency allowed in frequency adaptive metadynamicsFA_UPDATE_FREQUENCY=5000the frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACEFA_MIN_ACCELERATION=1e2 ... METADonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given herePrint quantities to a file. More detailsARG=p1the input for this action is the scalar output from one or more other actionsFILE=path.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=metadthe input for this action is the scalar output from one or more other actionsFILE=metad_data.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=d1.zthe input for this action is the scalar output from one or more other actionsFILE=distance_pocket.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=ort_up.*,ort_downthe input for this action is the scalar output from one or more other actionsFILE=barriers.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=500the frequency with which all the open files should be flushedENDPLUMEDTerminate plumed input. More details