[gmx-users] Heating error
mohammad reaza dayer
mrdayer at gmail.com
Sun Jan 31 13:40:07 CET 2010
Dear Justin
Greetings:
I want to melt up hemoglobin, using simulated annealing methods. I used the
following mdp file parameters:
****************************************************
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100000 ; total 100.0 ps.
tinit = 0
init_step = 0
nstcomm = 1
nstxout = 500 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 100
nstlog = 10
nstenergy = 100
nstlist = 100
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.08
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 8
ewald_rtol = 1e-5
optimize_fft = yes
nstcomm = 1
comm-grps = Protein Non-Protein
Tcoupl = no
tau-t = 0 0
tc-grps = Protein Non-Protein
ref-t = 310 310
solvent_optimization = sol
energygrps = Protein Non-Protein
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
gen_temp = 310
gen_seed = 173529
annealing = yes yes
annealing = single single
annealing_npoints = 100 100
annealing_time = 0 1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18 19 20 21
22 23 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 0 1 2 3 4 5 6 7
8 9 10 11 12 13 14 15 16 17 18 19 20
21 22 23 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
annealing_temp = 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
383 384 385 386 387 388 389 390 391 392 393
394 395 396 397 398 399 400 401 402 403 404
405 406 407 408 409 310 311 312 313 314 315
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
382 383 384 385 386 387 388 389 390 391 392
393 394 395 396 397 398 399 400 401 402 403
404 405 406 407 408 409 310
****************************************************************
the simulation started with no warning but unfortunately the protein
temperature increased for up to
2-3 ps and after that decreased to low temperatures. I have studies most of
e-mails in gmx-archives regarding such error and tried all of them but I
could not solve the problem. I will appreciate if your kindly help me.
Best Regards
dayer
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