[gmx-users] REMD analysis

[bharat gupta]

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