PLUMED-NEST

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

# restart
RESTART
Activate restart. More details
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-8844  # include toxin for appropriate RMSD/COM calcs

# groups
toxin: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=8824,8825,8826,8827,8828,8829,8830,8831,8838,8839,8842,8843,8844

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

# collective variables
380PRO_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=380PRO 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 380PRO_coord calculates a scalar quantity383LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=383LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 383LEU_coord calculates a scalar quantity384ILE_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=384ILE 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 384ILE_coord calculates a scalar quantity385LYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=385LYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 385LYS_coord calculates a scalar quantity386GLN_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=386GLN 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 386GLN_coord calculates a scalar quantity387ASN_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=387ASN 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 387ASN_coord calculates a scalar quantity388CYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=388CYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 388CYS_coord calculates a scalar quantity391PHE_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=391PHE 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 391PHE_coord calculates a scalar quantity399PHE_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=399PHE 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 399PHE_coord calculates a scalar quantity403LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=403LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 403LEU_coord calculates a scalar quantity406ARG_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=406ARG 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 406ARG_coord calculates a scalar quantity407TYR_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=407TYR 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 407TYR_coord calculates a scalar quantity410LYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=410LYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 410LYS_coord calculates a scalar quantity423SER_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=423SER 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 423SER_coord calculates a scalar quantity425ASN_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=425ASN 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 425ASN_coord calculates a scalar quantity426LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=426LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 426LEU_coord calculates a scalar quantity427GLY_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=427GLY 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 427GLY_coord calculates a scalar quantity428LYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=428LYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 428LYS_coord calculates a scalar quantity429VAL_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=429VAL 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 429VAL_coord calculates a scalar quantity430GLY_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=430GLY 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 430GLY_coord calculates a scalar quantity431SER_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=431SER 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 431SER_coord calculates a scalar quantity433CYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=433CYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 433CYS_coord calculates a scalar quantity434CYS_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=434CYS 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 434CYS_coord calculates a scalar quantity441ARG_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=441ARG 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 441ARG_coord calculates a scalar quantity442MET_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=442MET 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 442MET_coord calculates a scalar quantity445ALA_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=445ALA 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 445ALA_coord calculates a scalar quantity446GLU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=446GLU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 446GLU_coord calculates a scalar quantity448TYR_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=448TYR 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 448TYR_coord calculates a scalar quantity449LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=449LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 449LEU_coord calculates a scalar quantity452VAL_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=452VAL 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 452VAL_coord calculates a scalar quantity453LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=453LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 453LEU_coord calculates a scalar quantity480ARG_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=480ARG 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 480ARG_coord calculates a scalar quantity481ARG_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=481ARG 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 481ARG_coord calculates a scalar quantity484PHE_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=484PHE 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 484PHE_coord calculates a scalar quantity485SER_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=485SER 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 485SER_coord calculates a scalar quantity486ALA_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=486ALA 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03
The COORDINATION action with label 486ALA_coord calculates a scalar quantity487LEU_coord: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=487LEU 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=0.03


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

### toxin (heavy)
The COORDINATION action with label 487LEU_coord calculates a scalar quantitytoxin_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=toxin

### important residues from unbiased + experiment (heavy)
L383: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6012,6014,6016,6019,6021,6025,6029,6030
L383_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=L383

N387: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6089,6091,6093,6096,6097,6098,6101,6102
N387_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=N387

R406: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421
R406_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=R406

Y407: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442
Y407_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=Y407

K410: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6479,6481,6483,6486,6489,6492,6495,6499,6500
K410_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=K410

L426: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6732,6734,6736,6739,6741,6745,6749,6750
L426_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=L426

V429: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=6780,6782,6784,6786,6790,6794,6795
V429_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=V429

L449: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=7079,7081,7083,7086,7088,7092,7096,7097
L449_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=L449

S485: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=7653,7655,7657,7660,7662,7663
S485_com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=S485

### calph CENTER for relevant helices
helix1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the 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: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the 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: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=7533,7549,7563,7587,7619,7625,7635,7655,7666,7676

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

### protein-ligand dists
L383_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=L383_com,toxin_com
The DISTANCE action with label L383_com_dist calculates a scalar quantityL383_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=L383 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
N387_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=N387_com,toxin_com
The DISTANCE action with label N387_com_dist calculates a scalar quantityN387_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=N387 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
R406_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=R406_com,toxin_com
The DISTANCE action with label R406_com_dist calculates a scalar quantityR406_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=R406 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
Y407_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=Y407_com,toxin_com
The DISTANCE action with label Y407_com_dist calculates a scalar quantityY407_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=Y407 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
K410_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=K410_com,toxin_com
The DISTANCE action with label K410_com_dist calculates a scalar quantityK410_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K410 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
L426_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=L426_com,toxin_com
The DISTANCE action with label L426_com_dist calculates a scalar quantityL426_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=L426 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
V429_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=V429_com,toxin_com
The DISTANCE action with label V429_com_dist calculates a scalar quantityV429_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=V429 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
L449_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=L449_com,toxin_com
The DISTANCE action with label L449_com_dist calculates a scalar quantityL449_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=L449 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}
S485_com_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=S485_com,toxin_com
The DISTANCE action with label S485_com_dist calculates a scalar quantityS485_min_dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=S485 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=toxin 
MIN
calculate the minimum value
={BETA=100}

### protein-protein backbone distances
h1_h2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix1,helix2
The DISTANCE action with label h1_h2 calculates a scalar quantityh1_h3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix1,helix3
The DISTANCE action with label h1_h3 calculates a scalar quantityh2_h3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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!!!
The DISTANCE action with label h2_h3 calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1