mohammad reaza dayer wrote:
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.
It is useful to actually provide the link for any pertinent post for reference.
I think you're making the problem too complicated. Simulated annealing
increases the temperature linearly (per the manual), so I really see no need to
specify each time point individually, although I don't know why it doesn't work.
Simplify the problem:
annealing = yes yes
annealing = single single
annealing_npoints = 2 2
annealing_time = 0 100 0 100
annealing_temp = 310 409 310 409
In theory, the above should give you steadily-rising temperature over 100 ps.
-Justin
Best Regards
dayer
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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