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<p>Dear Justin<br>Greetings:</p>
<p>I want to melt up hemoglobin, using simulated annealing methods. I used the following mdp file parameters:<br>****************************************************<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 100000 ; total 100.0 ps.<br>tinit = 0<br>init_step = 0<br>nstcomm = 1<br>nstxout = 500 ; collect data every 0.5 ps<br>nstvout = 1000<br>nstfout = 100<br>
nstlog = 10<br>nstenergy = 100<br>nstlist = 100<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>
fourierspacing = 0.08<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 8<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>nstcomm = 1<br>comm-grps = Protein Non-Protein<br>
Tcoupl = no<br>tau-t = 0 0<br>tc-grps = Protein Non-Protein<br>ref-t = 310 310 <br>solvent_optimization = sol<br>energygrps = Protein Non-Protein<br>Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>gen_vel = no<br>gen_temp = 310 <br>gen_seed = 173529<br>annealing = yes yes<br>annealing = single single<br>
annealing_npoints = 100 100<br>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<br>
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<br>
****************************************************************<br>the simulation started with no warning but unfortunately the protein temperature increased for up to <br>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.<br>
Best Regards<br><font color="#888888">dayer </font></p></div><br>