[gmx-users] REMD Melting Curve
Justin Lemkul
jalemkul at vt.edu
Tue Mar 4 22:54:05 CET 2014
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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