**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

# restartRESTARTActivate restart. More detailsWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-8844 # include toxin for appropriate RMSD/COM calcsthe atoms that make up a molecule that you wish to align

# groupstoxin: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 detailsATOMS=8824,8825,8826,8827,8828,8829,8830,8831,8838,8839,8842,8843,8844the numerical indexes for the set of atoms in the group380PRO: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 detailsATOMS=5967,5968,5971,5974,5977,5979,5980the numerical indexes for the set of atoms in the group383LEU: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 detailsATOMS=6012,6014,6016,6019,6021,6025,6029,6030the numerical indexes for the set of atoms in the group384ILE:ATOMS=6031,6033,6035,6037,6041,6044,6048,6049the numerical indexes for the set of atoms in the group385LYS:ATOMS=6050,6052,6054,6057,6060,6063,6066,6070,6071the numerical indexes for the set of atoms in the group386GLN:ATOMS=6072,6074,6076,6079,6082,6083,6084,6087,6088the numerical indexes for the set of atoms in the group387ASN:ATOMS=6089,6091,6093,6096,6097,6098,6101,6102the numerical indexes for the set of atoms in the group388CYS:ATOMS=6103,6105,6107,6110,6111,6112the numerical indexes for the set of atoms in the group391PHE:ATOMS=6147,6149,6151,6154,6155,6157,6159,6161,6163,6165,6166the numerical indexes for the set of atoms in the group399PHE:ATOMS=6283,6285,6287,6290,6291,6293,6295,6297,6299,6301,6302the numerical indexes for the set of atoms in the group403LEU:ATOMS=6344,6346,6348,6351,6353,6357,6361,6362the numerical indexes for the set of atoms in the group406ARG:ATOMS=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421the numerical indexes for the set of atoms in the group407TYR:ATOMS=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442the numerical indexes for the set of atoms in the group410LYS:ATOMS=6479,6481,6483,6486,6489,6492,6495,6499,6500the numerical indexes for the set of atoms in the group423SER:ATOMS=6683,6685,6687,6690,6692,6693the numerical indexes for the set of atoms in the group425ASN:ATOMS=6718,6720,6722,6725,6726,6727,6730,6731the numerical indexes for the set of atoms in the group426LEU:ATOMS=6732,6734,6736,6739,6741,6745,6749,6750the numerical indexes for the set of atoms in the group427GLY:ATOMS=6751,6753,6756,6757the numerical indexes for the set of atoms in the group428LYS:ATOMS=6758,6760,6762,6765,6768,6771,6774,6778,6779the numerical indexes for the set of atoms in the group429VAL:ATOMS=6780,6782,6784,6786,6790,6794,6795the numerical indexes for the set of atoms in the group430GLY:ATOMS=6796,6798,6801,6802the numerical indexes for the set of atoms in the group431SER:ATOMS=6803,6805,6807,6810,6812,6813the numerical indexes for the set of atoms in the group433CYS:ATOMS=6836,6838,6840,6843,6844,6845the numerical indexes for the set of atoms in the group434CYS:ATOMS=6846,6848,6850,6853,6854,6855the numerical indexes for the set of atoms in the group441ARG:ATOMS=6956,6958,6960,6963,6966,6969,6971,6972,6975,6978,6979the numerical indexes for the set of atoms in the group442MET:ATOMS=6980,6982,6984,6987,6990,6991,6995,6996the numerical indexes for the set of atoms in the group445ALA:ATOMS=7021,7023,7025,7029,7030the numerical indexes for the set of atoms in the group446GLU:ATOMS=7031,7033,7035,7038,7041,7042,7043,7044,7045the numerical indexes for the set of atoms in the group448TYR:ATOMS=7058,7060,7062,7065,7066,7068,7070,7071,7073,7075,7077,7078the numerical indexes for the set of atoms in the group449LEU:ATOMS=7079,7081,7083,7086,7088,7092,7096,7097the numerical indexes for the set of atoms in the group452VAL:ATOMS=7125,7127,7129,7131,7135,7139,7140the numerical indexes for the set of atoms in the group453LEU:ATOMS=7141,7143,7145,7148,7150,7154,7158,7159the numerical indexes for the set of atoms in the group480ARG:ATOMS=7561,7563,7565,7568,7571,7574,7576,7577,7580,7583,7584the numerical indexes for the set of atoms in the group481ARG:ATOMS=7585,7587,7589,7592,7595,7598,7600,7601,7604,7607,7608the numerical indexes for the set of atoms in the group484PHE:ATOMS=7633,7635,7637,7640,7641,7643,7645,7647,7649,7651,7652the numerical indexes for the set of atoms in the group485SER:ATOMS=7653,7655,7657,7660,7662,7663the numerical indexes for the set of atoms in the group486ALA:ATOMS=7664,7666,7668,7672,7673the numerical indexes for the set of atoms in the group487LEU:ATOMS=7674,7676,7678,7681,7683,7687,7691,7692the numerical indexes for the set of atoms in the group

# collective variables380PRO_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms380PROGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function383LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms383LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function384ILE_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms384ILEGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function385LYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms385LYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function386GLN_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms386GLNGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function387ASN_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms387ASNGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function388CYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms388CYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function391PHE_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms391PHEGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function399PHE_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms399PHEGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function403LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms403LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function406ARG_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms406ARGGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function407TYR_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms407TYRGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function410LYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms410LYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function423SER_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms423SERGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function425ASN_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms425ASNGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function426LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms426LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function427GLY_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms427GLYGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function428LYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms428LYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function429VAL_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms429VALGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function430GLY_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms430GLYGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function431SER_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms431SERGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function433CYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms433CYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function434CYS_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms434CYSGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function441ARG_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms441ARGGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function442MET_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms442METGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function445ALA_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms445ALAGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function446GLU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms446GLUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function448TYR_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms448TYRGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function449LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms449LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function452VAL_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms452VALGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function453LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms453LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function480ARG_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms480ARGGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function481ARG_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms481ARGGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function484PHE_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms484PHEGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function485SER_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms485SERGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function486ALA_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms486ALAGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function487LEU_coord:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atoms487LEUGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)toxinD_0=0.27The d_0 parameter of the switching functionR_0=0.03The r_0 parameter of the switching function

############################################## ############## DEFINE RESIDUES ############### ##############################################

### toxin (heavy)toxin_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitiontoxin

### important residues from unbiased + experiment (heavy)L383:ATOMS=6012,6014,6016,6019,6021,6025,6029,6030the numerical indexes for the set of atoms in the groupL383_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionL383N387:ATOMS=6089,6091,6093,6096,6097,6098,6101,6102the numerical indexes for the set of atoms in the groupN387_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionN387R406:ATOMS=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421the numerical indexes for the set of atoms in the groupR406_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionR406Y407:ATOMS=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442the numerical indexes for the set of atoms in the groupY407_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionY407K410:ATOMS=6479,6481,6483,6486,6489,6492,6495,6499,6500the numerical indexes for the set of atoms in the groupK410_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionK410L426:ATOMS=6732,6734,6736,6739,6741,6745,6749,6750the numerical indexes for the set of atoms in the groupL426_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionL426V429:ATOMS=6780,6782,6784,6786,6790,6794,6795the numerical indexes for the set of atoms in the groupV429_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionV429L449:ATOMS=7079,7081,7083,7086,7088,7092,7096,7097the numerical indexes for the set of atoms in the groupL449_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionL449S485:ATOMS=7653,7655,7657,7660,7662,7663the numerical indexes for the set of atoms in the groupS485_com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the list of atoms which are involved the virtual atom's definitionS485

### calph CENTER for relevant heliceshelix1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5707,5722,5732,5753,5763,5785,5801,5821,5833,5848,5868,5898,5904,5923,5939,5954,5977,5983,6000,6014,6033,6052,6074,6091,6105,6115,6130,6149,6169,6184the list of atoms which are involved the virtual atom's definitionhelix2:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=6242,6263,6285,6305,6322,6336,6346,6365,6384,6400,6424,6445,6459,6481,6503the list of atoms which are involved the virtual atom's definitionhelix3:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=7533,7549,7563,7587,7619,7625,7635,7655,7666,7676the list of atoms which are involved the virtual atom's definition

############################################### ############### DEFINE COLVARS ################ ###############################################

### protein-ligand distsL383_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenL383_com,toxin_comL383_dist:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBL383GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueN387_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenN387_com,toxin_comN387_min_dist:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBN387GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueR406_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenR406_com,toxin_comR406_min_dist:DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBR406GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueY407_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenY407_com,toxin_comY407_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBY407GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueK410_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenK410_com,toxin_comK410_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBK410GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueL426_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenL426_com,toxin_comL426_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBL426GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueV429_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenV429_com,toxin_comV429_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBV429GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueL449_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenL449_com,toxin_comL449_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBL449GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum valueS485_com_dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenS485_com,toxin_comS485_min_dist:GROUPA=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBS485GROUPB=Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBtoxinMIN={BETA=100}calculate the minimum value

### protein-protein backbone distancesh1_h2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenhelix1,helix2h1_h3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenhelix1,helix3h2_h3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenhelix2,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!!!Print quantities to a file. More detailsFILE=COLVARthe name of the file on which to output these quantitiesARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1the frequency with which the quantities of interest should be output