[gmx-users] Continuing inturepted REMD simulation

[Mark Abraham]

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?
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>