[gmx-users] Re: REMD average acceptance ratio

[bharat gupta]

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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-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680