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 onv2.8
tested onmaster
# 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 383LEU_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 384ILE_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 385LYS_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 386GLN_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 387ASN_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 388CYS_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 391PHE_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 399PHE_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 403LEU_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 406ARG_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 407TYR_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 410LYS_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 423SER_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 425ASN_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 426LEU_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 427GLY_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 428LYS_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 429VAL_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 430GLY_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 431SER_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 433CYS_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 434CYS_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 441ARG_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 442MET_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 445ALA_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 446GLU_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 448TYR_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 449LEU_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 452VAL_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 453LEU_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 480ARG_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 481ARG_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 484PHE_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 485SER_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 486ALA_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 487LEU_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) toxin_com:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=S485
### calph CENTER for relevant helices helix1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 list of atoms which are involved the virtual atom's definition
=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 L383_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 N387_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 R406_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 Y407_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 K410_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 L426_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 V429_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 L449_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 S485_min_dist:
DISTANCES
Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of 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 h1_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 h2_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!!!
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