[gmx-users] REMD average acceptance ratio

Sat May 11 17:05:53 CEST 2013

Dear Sir,

Here's the temperature range that I got form t-remd :
1 300
2 323.7
3 348.75
4 375.23
5 403.22
6 432.83
7 464.14
8 497.24
9 532.26
10 569.32
11 608.51

according the above equation c should be somewhere around 2.37.

On Sat, May 11, 2013 at 11:10 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Well, actually things do not look so good. But is it possible that grace
> is actually no able to plot things correctly? You have line going
> throughout the plot from complete-left to complete-right!
>
> I am do not know what the t-rems calculator does but apparently it is not
> optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c),
> where T0 is close to your starting temperature and c is a constant that you
> can tune and will define the spacing between the temperatures. From your
> current data you can guess the spacing and thus the c value you need. Note
> that the exchange ratio is quickly converging in the simulation so you can
> make a few trials …
>
> On May 11, 2013, at 1:40 PM, bharat gupta <bharat.85.monu at gmail.com>
> wrote:
>
> > Dear Sir,
> >
> > Thank you for your reply. I choose the temperature distribution using
> > t-remd calculator. Here's the link for index and temp files .
> > https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
> > https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
> >
> >
> >
> >
> >
> >
> >
> > On Sat, May 11, 2013 at 12:04 AM, XAvier Periole <x.periole at rug.nl>
> wrote:
> >
> >>
> >> The replicas seem indeed to have exchange. Using a colour for the #
> >> replicas would help.
> >>
> >> I could not access to the first link.
> >>
> >> Note also that the increase of exchange ratio with the temperature
> suggest
> >> the distribution of the temperature is not optimal and may be with
> regular
> >> intervals? You want to use a exponential distribution.
> >>
> >> On May 10, 2013, at 4:53 PM, bharat gupta <bharat.85.monu at gmail.com>
> >> wrote:
> >>
> >>> Dear gmx members,
> >>>
> >>> I have posted the same question previously , but I didn't get any
> reply.
> >>> So, if anyone can help me out ...
> >>>
> >>> I performed a REMD simulation on a peptide 384 atoms (24 residues). In
> >>> total 11 replicas were simulated for a period of 50ns each. The
> exchange
> >>> was allwoed at every 1000 steps. 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
> >>> Repl      .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
> >>> Repl  number of exchanges:
> >>> Repl     0    1    2    3    4    5    6    7    8    9   10
> >>> Repl     2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
> >>> Repl  average number of exchanges:
> >>> Repl     0    1    2    3    4    5    6    7    8    9   10
> >>> Repl      .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
> >>>
> >>> The acceptance ratio for each replica and average acceptance ratio is
> as
> >>> calculated below :-
> >>>
> >>>               accp. ratio
> >>> 2038 0.16304
> >>> 2007 0.16056
> >>> 2065 0.1652
> >>> 2117 0.16936
> >>> 2182 0.17456
> >>> 2587 0.20696
> >>> 3022 0.24176
> >>> 3213 0.25704
> >>> 3554 0.28432
> >>> 3703 0.29624
> >>> 0.211904 (avg accp ratio) (Is this value correct ??)
> >>>
> >>> The Pdes used while generating temp. range was also 0.2. Does that mean
> >>> that  replicas have exchanged for the given temp.range ??.  Here's the
> >> link
> >>> for both remd_temp and remd_index files (
> >>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<
> >>
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810
> >>> )
> >>> , (
> >>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<
> >>
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810
> >>>
> >>> )
> >>>
> >>> --
> >>> Bharat
> >>> --
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> >>
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> >
> >
> >
> > --
> > Bharat
> > Ph.D. Candidate
> > Biomolecular Engineering Laboratory
> > Pusan National University
> > South Korea
> > Mobile no. - 010-5818-3680
> > --
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