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 details STRUCTUREa file in pdb format containing a reference structure=../input_files/first.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-6250 # Definition of the center of mass of the ligand, considering only its heavy atoms COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,5,6,10,14,17,18,19,22,23,24,25,26,29 LABELa label for the action so that its output can be referenced in the input to other actions=ixo
# Definition of the center of mass of the pocket COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1396,1398,1400,1403,1404,1406,1408,1409,1411,1413,1415,1416,1449,1451,1453,1456,1458,1459,1495,1497,1499,1501,1505,1509,1510,2838,2840,2842,2845,2846,2848,2850,2852,2854,2856,2857,3605,3607,3609,3612,3613,3615,3617,3618,3620,3622,3624,3625 LABELa label for the action so that its output can be referenced in the input to other actions=pkt DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ixo,pkt LABELa label for the action so that its output can be referenced in the input to other actions=d1 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances
# Restraining potential of the ligand DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ixo,pkt LABELa label for the action so that its output can be referenced in the input to other actions=restr NOPBC ignore the periodic boundary conditions when calculating distances sphere: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=restr ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=1000. #ligand ring: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=23,24,25,26,29 #ixo: COM ATOMS=1,5,6,10,14,17,18,19,22,23,24,25,26,29
# Trimetylammonium interactions ring244: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3971,3972,3974,3976,3979,3981 ring221: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3614,3615,3617,3619,3622,3624 ring86: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1405,1406,1408,1410,1413,1415 oxy85: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1394,1395 # Ligand ring interactions val93: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1501,1503,1507 ile160: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2605,2609,2612 thr169: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2740,2742,2746 # all ligand interactions trp218: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3566,3567,3569,3571,3572,3574,3576,3578,3580 cys158: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2572,2575 # Definition of the contact maps for the pathCV CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.324857000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.326715000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.317481000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.916788000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.988975000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.985199000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.459210000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.532785000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.151720000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm1 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.322060000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.322125000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.318081000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.940059000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.974572000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.912335000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.641878000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.522181000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.308574000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm2 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.320523000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.324186000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.315741000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.918387000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.782751000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.416873000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.918085000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.519385000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.736644000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm3 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.324818000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.316640000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.316240000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.922710000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.392776000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.178666000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.919086000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.532663000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.949034000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm4 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.326082000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.325629000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.303538000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.887596000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.143690000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.064591000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.999237000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.587326000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.878697000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm5 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.328269000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.327338000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.320984000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.914713000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.062782000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.033614000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.998120000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.734615000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.777428000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm6 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.326594000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.326341000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.321865000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.893738000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.049625000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.020003000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.996938000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.648535000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.469544000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm7 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.326402000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.324290000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.317068000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.765955000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.036467000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.015861000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.990764000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.636723000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.498470000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm8 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.216448000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.239333000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.182106000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.169182000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.008046000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.003324000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.674940000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.784664000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.083936000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm9 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.044800000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.032370000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.022490000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.041785000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.001275000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.000763000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.067223000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.764340000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.031289000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm10 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.010987000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.010682000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.007535000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.013361000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.000552000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.000381000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.024819000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.413170000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.018060000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm11 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ... ATOMS1the atoms involved in each of the contacts you wish to calculate=5,ring244 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE1A reference value for a given contact, by default is 0=0.000000000 WEIGHT1A weight value for a given contact, by default is 1=0.333 ATOMS2the atoms involved in each of the contacts you wish to calculate=5,ring221 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE2A reference value for a given contact, by default is 0=0.000000000 WEIGHT2A weight value for a given contact, by default is 1=0.333 ATOMS3the atoms involved in each of the contacts you wish to calculate=5,ring86 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE3A reference value for a given contact, by default is 0=0.000000000 WEIGHT3A weight value for a given contact, by default is 1=0.333 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,oxy85 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE4A reference value for a given contact, by default is 0=0.000000000 WEIGHT4A weight value for a given contact, by default is 1=1. ATOMS5the atoms involved in each of the contacts you wish to calculate=trp218,ring SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE5A reference value for a given contact, by default is 0=0.000000000 WEIGHT5A weight value for a given contact, by default is 1=1. ATOMS6the atoms involved in each of the contacts you wish to calculate=val93,ring SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 NN=6 MM=12} REFERENCE6A reference value for a given contact, by default is 0=0.000000000 WEIGHT6A weight value for a given contact, by default is 1=1. ATOMS7the atoms involved in each of the contacts you wish to calculate=ile160,ring SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=12} REFERENCE7A reference value for a given contact, by default is 0=0.000000000 WEIGHT7A weight value for a given contact, by default is 1=1. ATOMS8the atoms involved in each of the contacts you wish to calculate=5,cys158 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2 NN=6 MM=10} REFERENCE8A reference value for a given contact, by default is 0=0.000000000 WEIGHT8A weight value for a given contact, by default is 1=1. ATOMS9the atoms involved in each of the contacts you wish to calculate=thr169,ring SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=10} REFERENCE9A reference value for a given contact, by default is 0=0.000000000 WEIGHT9A weight value for a given contact, by default is 1=1. LABELa label for the action so that its output can be referenced in the input to other actions=cm12 CMDIST calculate the distance with respect to the provided reference contact map ... CONTACTMAP # Definition of the pathCV p1: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=cm1,cm2,cm3,cm4,cm5,cm6,cm7,cm8,cm9,cm10,cm11,cm12 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=9.778314 # 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 details ARGthe arguments on which the bias is acting=p1.z ATthe positions of the wall=0.23 KAPPAthe force constant for the wall=50000. ort_down: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.z ATthe positions of the wall=-0.2 KAPPAthe force constant for the wall=1000. # Frequency-Adaptive Metadynamics METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=p1.s,p1.z GRID_MINthe lower bounds for the grid=1.,-0.2 GRID_MAXthe upper bounds for the grid=12.,0.4 HEIGHTthe heights of the Gaussian hills=2 SIGMAthe widths of the Gaussian hills=0.05,0.01 BIASFACTORuse well tempered metadynamics and use this bias factor=20 LABELa label for the action so that its output can be referenced in the input to other actions=metad TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300. CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor FREQUENCY_ADAPTIVE Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor PACEthe frequency for hill addition=500 FA_MAX_PACEthe maximum hill addition frequency allowed in frequency adaptive metadynamics=50000 FA_UPDATE_FREQUENCYthe frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE=5000 FA_MIN_ACCELERATIONonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here=1e2 ... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.* FILEthe name of the file on which to output these quantities=path.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metad.* FILEthe name of the file on which to output these quantities=metad_data.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z FILEthe name of the file on which to output these quantities=distance_pocket.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ort_up.*,ort_down.* FILEthe name of the file on which to output these quantities=barriers.dat STRIDE the frequency with which the quantities of interest should be output=500 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500 ENDPLUMEDTerminate plumed input. More details