[gmx-users] REMD Melting Curve
atanu das
samrucu at yahoo.co.in
Tue Mar 4 18:24:41 CET 2014
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.
Atanu
On Tuesday, 4 March 2014 12:55 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On 2014-03-04 00:20, atanu_das wrote:
> Dear Gromacs users,
> I have performed a REMD simulation with 12 replicas
> exponentially spaced between 260-420K. However, when I applied g_kinetics
> program to generate the melting curve, I got 161 values starting from 260K
> to 420K having the folded fraction reported at each temperature. My question
> is if I am applying 12 replicas exponentially spaced in the temperature
> range chosen, how could I get 161 values? Am I doing something wrong? Does
> g_kinetics in GROMACS use any smoothing function to generate the
> intermediate temperature and folded fraction values?
> Please suggest/advise.
> Atanu
What kind of values? You get one fraction folded per replica, right?
Did you succesfully run the demux.pl?
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/REMD-Melting-Curve-tp5014920.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
--
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