[gmx-users] Re: REMD average acceptance ratio

[XAvier Periole]

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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