On 3/4/14, 11:26 PM, atanu das wrote:
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
There are no smoothing functions applied in the melting curve. It is a very
simple calculation relating probability to free energy. It should be very easy
to expand the code to create a profile over a greater temperature range, and
even make these command-line options for greater flexibility.
-Justin
On Tuesday, 4 March 2014 4:01 PM, Justin Lemkul <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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