[Spam:*****] [gmx-users] REMD analysis

[XAvier Periole]

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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