Project ID: plumID:20.011
Source: plumed.dat
Originally used with PLUMED version: 2.4
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
tested onv2.10
tested onmaster
# restart
RESTARTActivate restart. More details
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=1-8844  # include toxin for appropriate RMSD/COM calcs

# groups
toxin: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=8824,8825,8826,8827,8828,8829,8830,8831,8838,8839,8842,8843,8844

380PRO: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5967,5968,5971,5974,5977,5979,5980
383LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6012,6014,6016,6019,6021,6025,6029,6030
384ILE: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6031,6033,6035,6037,6041,6044,6048,6049
385LYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6050,6052,6054,6057,6060,6063,6066,6070,6071
386GLN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6072,6074,6076,6079,6082,6083,6084,6087,6088
387ASN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6089,6091,6093,6096,6097,6098,6101,6102
388CYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6103,6105,6107,6110,6111,6112
391PHE: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6147,6149,6151,6154,6155,6157,6159,6161,6163,6165,6166
399PHE: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6283,6285,6287,6290,6291,6293,6295,6297,6299,6301,6302
403LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6344,6346,6348,6351,6353,6357,6361,6362
406ARG: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421
407TYR: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442
410LYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6479,6481,6483,6486,6489,6492,6495,6499,6500
423SER: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6683,6685,6687,6690,6692,6693
425ASN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6718,6720,6722,6725,6726,6727,6730,6731
426LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6732,6734,6736,6739,6741,6745,6749,6750
427GLY: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6751,6753,6756,6757
428LYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6758,6760,6762,6765,6768,6771,6774,6778,6779
429VAL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6780,6782,6784,6786,6790,6794,6795
430GLY: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6796,6798,6801,6802
431SER: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6803,6805,6807,6810,6812,6813
433CYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6836,6838,6840,6843,6844,6845
434CYS: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6846,6848,6850,6853,6854,6855
441ARG: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6956,6958,6960,6963,6966,6969,6971,6972,6975,6978,6979
442MET: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6980,6982,6984,6987,6990,6991,6995,6996
445ALA: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7021,7023,7025,7029,7030
446GLU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7031,7033,7035,7038,7041,7042,7043,7044,7045
448TYR: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7058,7060,7062,7065,7066,7068,7070,7071,7073,7075,7077,7078
449LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7079,7081,7083,7086,7088,7092,7096,7097
452VAL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7125,7127,7129,7131,7135,7139,7140
453LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7141,7143,7145,7148,7150,7154,7158,7159
480ARG: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7561,7563,7565,7568,7571,7574,7576,7577,7580,7583,7584
481ARG: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7585,7587,7589,7592,7595,7598,7600,7601,7604,7607,7608
484PHE: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7633,7635,7637,7640,7641,7643,7645,7647,7649,7651,7652
485SER: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7653,7655,7657,7660,7662,7663
486ALA: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7664,7666,7668,7672,7673
487LEU: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7674,7676,7678,7681,7683,7687,7691,7692

# collective variables
380PRO_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=380PRO GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
383LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=383LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
384ILE_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=384ILE GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
385LYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=385LYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
386GLN_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=386GLN GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
387ASN_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=387ASN GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
388CYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=388CYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
391PHE_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=391PHE GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
399PHE_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=399PHE GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
403LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=403LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
406ARG_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=406ARG GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
407TYR_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=407TYR GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
410LYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=410LYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
423SER_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=423SER GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
425ASN_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=425ASN GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
426LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=426LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
427GLY_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=427GLY GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
428LYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=428LYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
429VAL_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=429VAL GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
430GLY_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=430GLY GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
431SER_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=431SER GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
433CYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=433CYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
434CYS_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=434CYS GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
441ARG_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=441ARG GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
442MET_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=442MET GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
445ALA_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=445ALA GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
446GLU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=446GLU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
448TYR_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=448TYR GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
449LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=449LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
452VAL_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=452VAL GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
453LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=453LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
480ARG_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=480ARG GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
481ARG_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=481ARG GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
484PHE_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=484PHE GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
485SER_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=485SER GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
486ALA_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=486ALA GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03
487LEU_coord: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=487LEU GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=toxin D_0 The d_0 parameter of the switching function=0.27 R_0The r_0 parameter of the switching function=0.03


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### toxin (heavy)
toxin_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=toxin

### important residues from unbiased + experiment (heavy)
L383: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6012,6014,6016,6019,6021,6025,6029,6030
L383_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=L383

N387: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6089,6091,6093,6096,6097,6098,6101,6102
N387_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=N387

R406: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421
R406_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=R406

Y407: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442
Y407_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=Y407

K410: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6479,6481,6483,6486,6489,6492,6495,6499,6500
K410_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=K410

L426: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6732,6734,6736,6739,6741,6745,6749,6750
L426_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=L426

V429: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6780,6782,6784,6786,6790,6794,6795
V429_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=V429

L449: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7079,7081,7083,7086,7088,7092,7096,7097
L449_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=L449

S485: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7653,7655,7657,7660,7662,7663
S485_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=S485

### calph CENTER for relevant helices
helix1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5707,5722,5732,5753,5763,5785,5801,5821,5833,5848,5868,5898,5904,5923,5939,5954,5977,5983,6000,6014,6033,6052,6074,6091,6105,6115,6130,6149,6169,6184
helix2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=6242,6263,6285,6305,6322,6336,6346,6365,6384,6400,6424,6445,6459,6481,6503
helix3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=7533,7549,7563,7587,7619,7625,7635,7655,7666,7676

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### protein-ligand dists
L383_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=L383_com,toxin_com
L383_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=L383 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
N387_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=N387_com,toxin_com
N387_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N387 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
R406_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=R406_com,toxin_com
R406_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=R406 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
Y407_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=Y407_com,toxin_com
Y407_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Y407 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
K410_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=K410_com,toxin_com
K410_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K410 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
L426_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=L426_com,toxin_com
L426_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=L426 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
V429_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=V429_com,toxin_com
V429_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=V429 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
L449_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=L449_com,toxin_com
L449_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=L449 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}
S485_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=S485_com,toxin_com
S485_min_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=S485 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=toxin MINcalculate the minimum value={BETA=100}

### protein-protein backbone distances
h1_h2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2
h1_h3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix3
h2_h3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix2,helix3

### linear combination of order parameters
#rc1: COMBINE ARG=L383_dist,N387_dist,R406_dist,Y407_dist,K410_dist,L426_dist,V429_dist,L449_dist,S485_dist,h1_h2,h1_h3,h2_h3 PERIODIC=NO COEFFICIENTS=0,0,0,0,0,0,0,0,0,1,0,0

# make STRIDE = to your exchange attempt frequency!!!
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1