Project ID: plumID:20.005
Source: input_data/classical/WT-metaD/WT-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. # Well-Tempered Metadynamics METADUsed to performed metadynamics on one or more collective variables. 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=1.5 SIGMAthe widths of the Gaussian hills=0.05,0.01 BIASFACTORuse well tempered metadynamics and use this bias factor=25 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] PACEthe frequency for hill addition=500 # 1ps WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR FILE a file in which the list of added hills is stored=../HILLS ... 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=p1.*,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