[gmx-users] REMD average acceptance ratio

[XAvier Periole]

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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