[gmx-users] Continuing inturepted REMD simulation

[Nizar Masbukhin]

So, in REMD case, we can not continue simulation if it interrupted?

and, How do I check wether exchange occurred or not?

On Tue, Dec 2, 2014 at 7:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You'll certainly lose the per-run statistics, because nobody's cared enough
> to write the code to accumulate it over interrupted runs.
>
> Showing no exchanges at all is another problem, but
> *you should look at the actual exchange reports to see whether the problem
> is that no exchanges*
> occurred, or that the books weren't being kept properly.
>
> Mark
>
> On Tue, Dec 2, 2014 at 6:59 AM, Nizar Masbukhin <nizar.fkub08 at gmail.com>
> wrote:
>
> > Dear gromacs users,
> > I have finished an REMD simulation, tough it had interupted (by
> electrical
> > instabilty that lead computer shutdown) several times.  I continue the
> > interupted simulation using this command:
> > mpirun -np 8 mdrun_mpi -v -multidir md[01234567] -replex 2000 -cpt 3 -cpi
> > state.cpt
> >
> > however, the remd statistics show unexpected exchange probability.
> > Replica exchange statistics
> > Repl  3365 attempts, 1683 odd, 1682 even
> > Repl  average probabilities:
> > Repl     0    1    2    3    4    5    6    7
> > Repl
> > Repl  number of exchanges:
> > Repl     0    1    2    3    4    5    6    7
> > Repl        0    0    0    0    0    0    0
> > Repl  average number of exchanges:
> > Repl     0    1    2    3    4    5    6    7
> > Repl      .00  .00  .00  .00  .00  .00  .00
> >
> >
> > Repl                                Empirical Transition Matrix
> > Repl       1       2       3       4       5       6       7       8
> > Repl  1.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0
> > Repl  0.0000  1.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  1
> > Repl  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  0.0000  0.0000  2
> > Repl  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  0.0000  3
> > Repl  0.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  4
> > Repl  0.0000  0.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  5
> > Repl  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  1.0000  0.0000  6
> > Repl  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  1.0000  7
> >
> > That statistics was very different when i try remd simulation with short
> > timesteps, and uninterupted one. the exchange probabilty was 0.3 as i
> > expected.
> > Could anyone tell me whats wrong?
> > --
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-- 
Thanks