[gmx-users] REMD Melting Curve
atanu das
samrucu at yahoo.co.in
Wed Mar 5 05:29:13 CET 2014
Thanks Justin. That's reassuring. However, I was wondering if any smoothing function is used in getting the melted fractions at intermediate temperatures with 1-K resolution. I could not find it in the description of the g_kinetics program. I need to know this because - (1) to justify my result to a person who would ask how I am getting values more than the number of replicas being used and (2) if I know the smoothing function then I would be able to estimate the temperature when folded fraction f=0. Because then I would be able to extract the free energy of complete unfolding as currently the melted fraction stops as 0.278.
-Atanu
On Tuesday, 4 March 2014 4:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 3/4/14, 12:22 PM, atanu das wrote:
> Dear Sir,
> I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below ......
>
> # This file was created Wed Feb 26 10:10:27 2014
> # by the following command:
> # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg
> #
> # g_kinetics_d is part of G R O M A C S:
> #
> # Groningen Machine for Chemical Simulation
> #
> @ title "Melting curve"
> @ xaxis label "T (K)"
> @ yaxis label ""
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Folded fraction"
> @ s1 legend "DG (kJ/mole)"
> 260 0.929 5.556
> 261 0.927 5.500
> 262 0.924 5.445
> 263 0.922 5.389
> 264 0.919 5.334
> 265 0.916 5.278
> 266 0.914 5.223
> 267 0.911 5.167
> 268 0.908 5.112
> 269 0.906 5.056
> 270 0.903 5.000
> 271 0.900 4.945
> 272 0.897 4.889
> 273 0.894 4.834
> 274 0.891 4.778
> 275 0.888 4.723
> 276 0.884 4.667
>
277 0.881 4.612
> 278 0.878 4.556
> 279 0.874 4.500
> 280 0.871 4.445
> 281 0.867 4.389
> 282 0.864 4.334
> 283 0.860 4.278
> 284 0.857 4.223
> 285 0.853 4.167
> 286 0.849 4.112
> 287 0.845 4.056
> 288 0.842 4.000
> 289 0.838
3.945
> 290 0.834 3.889
> 291 0.830 3.834
> 292 0.826 3.778
> 293 0.822 3.723
> 294 0.818 3.667
> 295 0.813 3.612
> 296 0.809 3.556
> 297 0.805 3.500
> 298 0.801 3.445
> 299 0.796 3.389
> 300 0.792 3.334
> 301 0.787 3.278
> 302 0.783 3.223
> 303 0.779 3.167
> 304 0.774 3.112
> 305 0.769 3.056
> 306 0.765 3.000
> 307 0.760 2.945
> 308 0.756 2.889
> 309 0.751 2.834
> 310 0.746 2.778
> 311 0.741 2.723
> 312 0.737 2.667
> 313 0.732 2.612
>
314 0.727 2.556
> 315 0.722 2.500
> 316 0.717 2.445
> 317 0.712 2.389
> 318 0.707 2.334
> 319 0.702 2.278
> 320 0.697 2.223
> 321 0.693 2.167
> 322 0.688 2.112
> 323 0.683 2.056
> 324 0.678 2.001
> 325 0.673 1.945
> 326 0.668
1.889
> 327 0.663 1.834
> 328 0.657 1.778
> 329 0.652 1.723
> 330 0.647 1.667
> 331 0.642 1.612
> 332 0.637 1.556
> 333 0.632 1.501
> 334 0.627 1.445
> 335 0.622 1.389
> 336 0.617 1.334
> 337 0.612 1.278
> 338 0.607 1.223
> 339 0.602 1.167
> 340 0.597 1.112
> 341 0.592 1.056
> 342 0.587 1.001
> 343 0.582 0.945
> 344 0.577 0.889
> 345 0.572 0.834
> 346 0.567 0.778
> 347 0.562 0.723
> 348 0.557 0.667
> 349 0.553 0.612
> 350 0.548 0.556
>
351 0.543 0.501
> 352 0.538 0.445
> 353 0.533 0.389
> 354 0.528 0.334
> 355 0.524 0.278
> 356 0.519 0.223
> 357 0.514 0.167
> 358 0.509 0.112
> 359 0.505 0.056
> 360 0.500 0.001
> 361 0.495 -0.055
> 362 0.491 -0.111
> 363 0.486
-0.166
> 364 0.482 -0.222
> 365 0.477 -0.277
> 366 0.473 -0.333
> 367 0.468 -0.388
> 368 0.464 -0.444
> 369 0.459 -0.499
> 370 0.455 -0.555
> 371 0.451 -0.611
> 372 0.446 -0.666
> 373 0.442 -0.722
> 374 0.438 -0.777
> 375 0.434 -0.833
> 376 0.429 -0.888
> 377 0.425 -0.944
> 378 0.421 -0.999
> 379 0.417 -1.055
> 380 0.413 -1.111
> 381 0.409 -1.166
> 382 0.405 -1.222
> 383 0.401 -1.277
> 384 0.397 -1.333
> 385 0.393 -1.388
> 386 0.389 -1.444
> 387 0.386 -1.499
>
388 0.382 -1.555
> 389 0.378 -1.610
> 390 0.374 -1.666
> 391 0.371 -1.722
> 392 0.367 -1.777
> 393 0.363 -1.833
> 394 0.360 -1.888
> 395 0.356 -1.944
> 396 0.353 -1.999
> 397 0.349 -2.055
> 398 0.346 -2.110
> 399 0.342 -2.166
> 400 0.339
-2.222
> 401 0.336 -2.277
> 402 0.332 -2.333
> 403 0.329 -2.388
> 404 0.326 -2.444
> 405 0.323 -2.499
> 406 0.319 -2.555
> 407 0.316 -2.610
> 408 0.313 -2.666
> 409 0.310 -2.722
> 410 0.307 -2.777
> 411 0.304 -2.833
> 412 0.301 -2.888
> 413 0.298 -2.944
> 414 0.295 -2.999
> 415 0.292 -3.055
> 416 0.289 -3.110
> 417 0.286 -3.166
> 418 0.284 -3.222
> 419 0.281 -3.277
> 420 0.278 -3.333
>
> So, as you can see, I got folded fraction and associated free energy change at each temperature ranging from 260-420K.
This is exactly what g_kinetics is supposed to do. It is hard-coded to produce
a melting curve at 1-K intervals from 260K to
420K, for whatever reason. It
could easily be changed by modifying the code, but as far as I can see, this is
the expected behavior.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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