[gmx-users] Continuing inturepted REMD simulation

[Mark Abraham]

On Wed, Dec 3, 2014 at 2:33 PM, Nizar Masbukhin <nizar.fkub08 at gmail.com>
wrote:

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

No, that's not what I said.


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

See
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B#

those 'x' show an exchange happening.

Mark


> 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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