On Fri, Feb 27, 2015 at 12:07 PM, Abhi Acharya
wrote:
> Hello GROMACS users,
>
> I have a problem with the Replica Exchange statistics printed in log file.
> I ran a 25 ns Replica exchange on a cluster through a queuing system.
> However, due to insufficient wall time the job stopped abruptly around 24
> ns and no stats were printed in the log file. I then extended the run by
> 1 steps using -nsteps and provided additional -cpi flag for
> continuation. The simulation ran without errors but the replica exchange
> stats that were printed in the log files of each of the replica is as
> follows:
>
> Replica exchange statistics
> Repl 10 attempts, 5 odd, 5 even
> Repl average probabilities:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
> 29 30 31
> Repl .23 .45 .57 .12 .28 .20 .82 .46 .44 .50 .07 .74 .53
> .46 .44 .51 .22 .56 .24 .56 .23 .82 .30 .28 .59 .54 .34 .53
> .75 .29 .62
> Repl number of exchanges:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
> 29 30 31
> Repl1230024222043
> 224140324102421
> 412
> Repl average number of exchanges:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
> 29 30 31
> Repl .20 .40 .60 .00 .00 .40 .80 .40 .40 .40 .00 .80 .60
> .40 .40 .80 .20 .80 .00 .60 .40 .80 .20 .00 .40 .80 .40 .20
> .80 .20 .40
>
>
>
> I rate of exchange attempt used was 1000, which means that the above stats
> somehow only take into account the last 1 steps of the simulations. Is
>
This is normal. The subsequent mdrun will not read from the old .log file,
and the data is not in the checkpoint.
> this some bug or I did something wrong ? More importantly, is there a way
> to regenerate the replica exchange stats from the log file ?
>
Not without writing a custom script to parse the per-exchange information.
Mark
>
> Regards,
> Abhishek Acharya
> Shasara Research Foundation
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