[Spam:*****] [gmx-users] REMD analysis
bharat gupta
bharat.85.monu at gmail.com
Thu May 16 14:04:44 CEST 2013
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611
Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649
md.log files output from three different trials:
Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31
Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31
Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22
I think as the required acceptance value all the three trials are fine, but
trail 3 would be much better to continue the further runs and anlysis ??
So, is it fine to continue with the third simulation ?? But still the
problem is that I am not getting the exact graphs with xmgrace??
On Thu, May 16, 2013 at 5:36 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> You have to convince yourself, not me :)) But I can give you my opinion …
>
> On May 16, 2013, at 10:33 AM, bharat gupta <bharat.85.monu at gmail.com>
> wrote:
>
> > Okay Sir, I will try two-three combinations this time and will report
> back
> > to you ...
> >
> >
> > On Thu, May 16, 2013 at 5:25 PM, XAvier Periole <x.periole at rug.nl>
> wrote:
> >
> >>
> >> An acceptance ratio of 0.2/0.3 is normally best. The problem with high
> >> acceptance ratio is that it means that a large portion of the exchanges
> are
> >> just back and forth exchanges between consecutive exchange and are thus
> >> disturbing the system more that actually helping sampling.
> >>
> >> I do not know particularly the paper you mention but if you like what
> they
> >> do, it is your choice at the end.
> >>
> >> Why don;t you just increase the spacing between the replicas? You will
> >> need less replicas and potentially you could run two simulations
> instead of
> >> one and evaluate the convergence ...
> >>
> >> On May 16, 2013, at 1:50 AM, bharat gupta <bharat.85.monu at gmail.com>
> >> wrote:
> >>
> >>> The plots that I showed in my last mail were for all replicas. I tried
> >>> plotting the first 500 ps of replica_index and replica_time files. I
> >> think
> >>> the plots look fine, and there could be problem with the plotting tool
> .
> >>> Here the link for both files ,
> >>> https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp
> >>> https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp
> >>>
> >>> Now regarding the high acceptance ratio which is 0.5 , I came across a
> >>> paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they
> have
> >>> mentioned that their average acceptance ratio ranged between 30 to
> 80%. I
> >>> have a question here, how did they calculate the range for the average
> >>> acceptance ratio or is it average ratio for each replica . Actually,
> this
> >>> is the reference I am following. I am also interested in peptide
> folding
> >>> simulation, similar to this article.
> >>>
> >>> I want to know, whether the average acceptance ratio that I have got
> for
> >> my
> >>> trial simulation is correct , together with the replica_temp and
> >>> replica_remd plots. Can I proceed for large production runs to complete
> >> my
> >>> experiment ??
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, May 14, 2013 at 6:34 PM, XAvier Periole <x.periole at rug.nl>
> >> wrote:
> >>>
> >>>>
> >>>> The interval between the exchange trial affect the efficiency of REMD
> >> but
> >>>> not the the exchange ratio (at least in principle).
> >>>>
> >>>> In you case I am not sure what the plot are showing! Are these showing
> >> all
> >>>> the replicas? what are the units?
> >>>>
> >>>> On May 14, 2013, at 5:07 AM, bharat gupta <bharat.85.monu at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> Dear Sir,
> >>>>>
> >>>>> Here's the result for the REMD trial with large temperature gaps.
> >>>>>
> >>>>> Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9
> >>>> 424.4
> >>>>> 447.1 471.0 496.1 522.6 550.5 579.9 610.8
> >>>>>
> >>>>> Out of md16.log :
> >>>>>
> >>>>> Replica exchange statistics
> >>>>> Repl 249 attempts, 125 odd, 124 even
> >>>>> Repl average probabilities:
> >>>>> Repl 0 1 2 3 4 5 6 7 8 9 10 11
> 12
> >>>>> 13 14 15
> >>>>> Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45
> >> .47
> >>>>> .44 .46
> >>>>>
> >>>>> Repl number of exchanges:
> >>>>> Repl 0 1 2 3 4 5 6 7 8 9 10 11
> 12
> >>>>> 13 14 15
> >>>>> Repl 50 42 46 52 57 40 58 49 42 53 61 63
> >> 56
> >>>>> 57 58
> >>>>>
> >>>>> Repl average number of exchanges:
> >>>>> Repl 0 1 2 3 4 5 6 7 8 9 10 11
> 12
> >>>>> 13 14 15
> >>>>> Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51
> >> .45
> >>>>> .46 .46
> >>>>> Average acceptance ratio : 0.46
> >>>>>
> >>>>> But, the repli_index.xvg and replica_temp.xvg files still shows that
> >> the
> >>>>> replicas does not exchange equally well .
> >>>>>
> >>>>> https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png
> >>>>> https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
> >>>>>
> >>>>> what could be wrong in this case?? Is it the mdp file settings or
> >>>> implicit
> >>>>> solvent setting. Does the time to replica to exhange also affects
> their
> >>>>> swapping ??
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Tue, May 14, 2013 at 12:24 AM, XAvier Periole <x.periole at rug.nl>
> >>>> wrote:
> >>>>>
> >>>>>>
> >>>>>> You need to increase the temperature gaps indeed if you want
> >> acceptance
> >>>>>> ratio ~0.2/0.3. But again this won't work with the water …
> >>>>>>
> >>>>>> It is not clear what happens in your index file but probably a
> problem
> >>>>>> from grace to plot so many points … you can try to increase the "Max
> >>>>>> drawing path length" in the preference menu of grace.
> >>>>>>
> >>>>>> On May 13, 2013, at 4:22 PM, bharat gupta <bharat.85.monu at gmail.com
> >
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Dear Sir,
> >>>>>>>
> >>>>>>> I repeated the simulation again for 25 replicas with the following
> >>>> temp.
> >>>>>>> distribution .
> >>>>>>>
> >>>>>>> 280
> >>>>>>> 289.1
> >>>>>>> 298.5
> >>>>>>> 308.2
> >>>>>>> 318.2
> >>>>>>> 328.6
> >>>>>>> 339.3
> >>>>>>> 350.3
> >>>>>>> 361.7
> >>>>>>> 373.5
> >>>>>>> 385.6
> >>>>>>> 398.1
> >>>>>>> 411.1
> >>>>>>> 424.4
> >>>>>>> 438.3
> >>>>>>> 452.5
> >>>>>>> 467.2
> >>>>>>> 482.4
> >>>>>>> 498.1
> >>>>>>> 514.3
> >>>>>>> 531.0
> >>>>>>> 548.3
> >>>>>>> 566.1
> >>>>>>> 584.5
> >>>>>>> 603.5
> >>>>>>> 623.2
> >>>>>>>
> >>>>>>> The output of md.log file is :-
> >>>>>>>
> >>>>>>> Replica exchange statistics
> >>>>>>> Repl 24999 attempts, 12500 odd, 12499 even
> >>>>>>> Repl average probabilities:
> >>>>>>> Repl 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
> >>>>>>> Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58
> .59
> >>>> .59
> >>>>>>> .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66
> >>>>>>>
> >>>>>>> Repl number of exchanges:
> >>>>>>> Repl 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
> >>>>>>> Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312
> 7424
> >>>> 7408
> >>>>>>> 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
> >>>>>>>
> >>>>>>> Repl average number of exchanges:
> >>>>>>> Repl 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
> >>>>>>> Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58
> .59
> >>>> .59
> >>>>>>> .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66
> >>>>>>>
> >>>>>>> The average acceptance ration is around 0.6 which is still high.
> >>>>>>>
> >>>>>>> The link for replica_temp,replica_index :
> >>>>>>> https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png
> >>>>>>> https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png
> >>>>>>>
> >>>>>>> The temp files look better but the index file looks weird ...
> >>>>>>>
> >>>>>>> Do i need to experiment with the gap difference in order to get the
> >>>>>>> required ration of 0.2-0.3 ?? There is some problem with the .mdp
> >> file
> >>>>>>> settings??
> >>>>>>>
> >>>>>>> --
> >>>>>>> Bharat
> >>>>>>> --
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