I/O of molecular dynamics trajectory#
Check if FishMol is successfully installed#
!fishmol
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▀▀▄ Contact: Lei.Lei@durham.ac.uk
from fishmol import trj
from fishmol import vis
Read trajectory file#
You will need to specify your unit cell (supercell) or simulation box
You should specify the timestep of your trajectory, by default it is 5 fs
%%time
cell= [
[21.2944000000, 0.0000000000, 0.0000000000],
[-4.6030371123, 20.7909480472, 0.0000000000],
[-0.9719093466, -1.2106211379, 15.1054299403]
]
traj = trj.Trajectory(timestep = 5, data = "test/cage1_test_traj.xyz", index = ":", cell = cell)
CPU times: user 217 ms, sys: 10.6 ms, total: 228 ms
Wall time: 228 ms
View your system#
vis.render_atoms(traj.frames[0]) # Press 'A' to centre the view, left: rotate, right: zoom, middle: move
Retrieve the frames of the trajectory#
traj.frames[1] # The first frame in the trajectory, which is an fishmol Atoms object
Atoms(<generator object Atoms.__new__.<locals>.<genexpr> at 0x7fef095d1900>,
dtype=object)
Get the atomic symbol and position#
traj.frames[1].symbs
array(['F', 'F', 'F', 'O', 'O', 'C', 'C', 'F', 'F', 'F', 'O', 'O', 'C',
'C', 'O', 'H', 'H', 'O', 'H', 'H', 'N', 'N', 'N', 'N', 'O', 'H',
'H', 'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'C', 'H',
'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C',
'C', 'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H',
'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C',
'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'C',
'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H',
'H', 'C', 'H', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H',
'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'H', 'F',
'F', 'F', 'O', 'O', 'C', 'C', 'F', 'F', 'F', 'O', 'O', 'C', 'C',
'O', 'H', 'H', 'O', 'H', 'H', 'N', 'N', 'N', 'N', 'O', 'H', 'H',
'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'C', 'H', 'C',
'H', 'C', 'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C',
'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C',
'H', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'C',
'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'C', 'H',
'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H',
'C', 'H', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C',
'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'H', 'F', 'F',
'F', 'O', 'O', 'C', 'C', 'F', 'F', 'F', 'O', 'O', 'C', 'C', 'O',
'H', 'H', 'O', 'H', 'H', 'N', 'N', 'N', 'N', 'O', 'H', 'H', 'H',
'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'C', 'H', 'C', 'H',
'C', 'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H',
'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H',
'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H',
'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H',
'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C',
'H', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C',
'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'H', 'F', 'F', 'F',
'O', 'O', 'C', 'C', 'F', 'F', 'F', 'O', 'O', 'C', 'C', 'O', 'H',
'H', 'O', 'H', 'H', 'N', 'N', 'N', 'N', 'O', 'H', 'H', 'H', 'H',
'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'C', 'H', 'C', 'H', 'C',
'H', 'C', 'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C',
'H', 'C', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C',
'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'C',
'H', 'C', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H', 'C',
'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H',
'H', 'C', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'C', 'C',
'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'H'], dtype='<U2')
traj.frames[1].pos
array([[ 7.75433428, 19.22969115, 7.25789922],
[ 7.38459724, 17.89872552, 5.49949104],
[ 6.01174112, 17.83305553, 7.17866554],
...,
[-6.55112186, 13.02095143, 1.36287726],
[-6.47623272, 11.92016128, 1.43990435],
[-2.75848988, 12.44274372, 3.11918468]])
Calibrate the position by centre of mass#
Simply use the calib function
calibrated_traj = traj.calib()
calibrated_traj.frames[1].pos
array([[ 7.75432882, 19.22971761, 7.25787368],
[ 7.38459178, 17.89875198, 5.4994655 ],
[ 6.01173566, 17.83308199, 7.17864 ],
...,
[-6.55112732, 13.02097789, 1.36285172],
[-6.47623818, 11.92018774, 1.43987881],
[-2.75849534, 12.44277018, 3.11915914]])
Wrap into simulation box#
traj.wrap2box()
<fishmol.trj.Trajectory at 0x7fef09572280>
vis.render_atoms(traj.frames[0])
Save trajectory as xyz file#
traj.write(filename = "test/cage1_test_wrapped.xyz")
Read the file just saved#
traj_1 = traj = trj.Trajectory(timestep = 5, data = "test/cage1_test_wrapped.xyz", index = ":", cell = cell)
vis.render_atoms(traj_1.frames[0])
Molecule recognition#
cell= [
[21.2944000000, 0.0000000000, 0.0000000000],
[-4.6030371123, 20.7909480472, 0.0000000000],
[-0.9719093466, -1.2106211379, 15.1054299403]
]
traj = trj.Trajectory(timestep = 5, data = "test/cage1_test_traj.xyz", index = ":", cell = cell)
from fishmol.sel_tools import cluster
molecules = cluster(traj.frames[0], mic = True)
molecules
[Molecule(formula='O2F3C2', at_idx=[0, 1, 2, 3, 4, 5, 6]),
Molecule(formula='O2F3C2', at_idx=[7, 8, 9, 10, 11, 12, 13]),
Molecule(formula='H2O', at_idx=[16, 14, 15]),
Molecule(formula='H2O', at_idx=[17, 18, 19]),
Molecule(formula='H104O2N8C104', at_idx=[512, 513, 514, 515, 20, 21, 22, 23, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 278, 279, 280, 281, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511]),
Molecule(formula='H104O2N8C104', at_idx=[24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 149, 150, 151, 152, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 407, 408, 409, 410]),
Molecule(formula='O2F3C2', at_idx=[129, 130, 131, 132, 133, 134, 135]),
Molecule(formula='O2F3C2', at_idx=[136, 137, 138, 139, 140, 141, 142]),
Molecule(formula='H2O', at_idx=[144, 145, 143]),
Molecule(formula='H2O', at_idx=[146, 147, 148]),
Molecule(formula='O2F3C2', at_idx=[258, 259, 260, 261, 262, 263, 264]),
Molecule(formula='O2F3C2', at_idx=[265, 266, 267, 268, 269, 270, 271]),
Molecule(formula='H2O', at_idx=[272, 273, 274]),
Molecule(formula='H2O', at_idx=[275, 276, 277]),
Molecule(formula='O2F3C2', at_idx=[387, 388, 389, 390, 391, 392, 393]),
Molecule(formula='O2F3C2', at_idx=[394, 395, 396, 397, 398, 399, 400]),
Molecule(formula='H2O', at_idx=[401, 402, 403]),
Molecule(formula='H2O', at_idx=[404, 405, 406])]
You can pass the atom indices to the frame of a trajectory to access the information of the molecule
# e.g. view the second molecule
vis.render_atoms(traj.frames[0][molecules[4].at_idx])
vis.render_atoms(traj.frames[0][molecules[5].at_idx])
Filter trajectory#
Select by atomic symbol#
idx, atoms = traj.frames[0].at_sel(["O","H"])
print(idx)
Keep waters in the trajectory only#
waters = [mol.at_idx for mol in molecules if mol.formula == "H2O"]
waters = [idx for at_idx in waters for idx in at_idx]
waters
[16,
14,
15,
17,
18,
19,
144,
145,
143,
146,
147,
148,
272,
273,
274,
275,
276,
277,
401,
402,
403,
404,
405,
406]
traj.frames[0][waters]
Atoms(<generator object Atoms.__new__.<locals>.<genexpr> at 0x7fd66e4fe430>,
dtype=object)
vis.render_atoms(traj.frames[0][waters])
water_frames = [frame[waters] for frame in traj.frames]
traj.frames = water_frames
vis.render_atoms(traj.frames[0])