[gmx-users] issue in replica exchange

Mark Abraham mark.j.abraham at gmail.com
Fri Apr 26 09:21:36 CEST 2013 

On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Thanks for the answer. I'll check gmx4.5.7 and report back.
>
> I am not sure what you mean by GROMACS swaps the coordinates not the
> ensemble data. The coupling to P and T and not exchanged with it?


The code in src/kernel/repl_ex.c:

static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
{
    /* When t_state changes, this code should be updated. */
    int ngtc, nnhpres;
    ngtc    = state->ngtc * state->nhchainlength;
    nnhpres = state->nnhpres* state->nhchainlength;
    exchange_rvecs(ms, b, state->box, DIM);
    exchange_rvecs(ms, b, state->box_rel, DIM);
    exchange_rvecs(ms, b, state->boxv, DIM);
    exchange_reals(ms, b, &(state->veta), 1);
    exchange_reals(ms, b, &(state->vol0), 1);
    exchange_rvecs(ms, b, state->svir_prev, DIM);
    exchange_rvecs(ms, b, state->fvir_prev, DIM);
    exchange_rvecs(ms, b, state->pres_prev, DIM);
    exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
    exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
    exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
    exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
    exchange_doubles(ms, b, state->therm_integral, state->ngtc);
    exchange_rvecs(ms, b, state->x, state->natoms);
    exchange_rvecs(ms, b, state->v, state->natoms);
    exchange_rvecs(ms, b, state->sd_X, state->natoms);
}

I mis-stated last night - there *is* exchange of ensemble data, but it is
incomplete. In particular, state->ekinstate is not exchanged. Probably it
is incomplete because the 9-year-old comment about t_state changing is in a
location that nobody changing t_state will see. And serializing a complex C
data structure over MPI is tedious at best. But that is not really an
excuse for the non-modularity GROMACS has for many of its key data
structures. We are working on various workflow and actual code structure
improvements to fix/prevent issues like this, but the proliferation of
algorithms that ought to be inter-operable makes the job pretty hard.

Other codes seem to exchange the ensemble label data (e.g. reference
temperatures for T-coupling) because they write trajectories that are
continuous with respect to atomic coordinates. I plan to move REMD in
GROMACS to this approach, because it scales better, but it will not happen
any time soon.

That would explain what I see, but let see what 4.5.7 has to say first.
>

Great. It may be that there were other issues in 4.5.3 that exacerbated any
REMD problem.

Mark

Tks.
>
> On Apr 25, 2013, at 22:40, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > Thanks for the good report. There have been some known issues about the
> > timing of coupling stages with respect to various intervals between
> GROMACS
> > events for some algorithms. There are a lot of fixed problems in 4.5.7
> that
> > are not specific to REMD, but I have a few lingering doubts about whether
> > we should be exchanging (scaled) coupling values along with the
> > coordinates. (Unlike most REMD implementations, GROMACS swaps the
> > coordinates, not the ensemble data.) If you can reproduce those kinds of
> > symptoms in 4.5.7 (whether or not they then crash) then there looks like
> > there may be a problem with the REMD implementation that is perhaps
> evident
> > only with the kind of large time step Martini takes?
> >
> > Mark
> >
> >
> > On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole <x.periole at rug.nl>
> wrote:
> >
> >>
> >> Hi,
> >>
> >> I have been recently using the REMD code in gmx-407 and gmx-453 and got
> a
> >> few systems crashing for unclear reasons so far. The main tests I made
> are
> >> using gmx407 but it is all reproducible with gmx453. The crashing was
> also
> >> reproduced (not necessarily at the same time point) on several
> >> architectures.
> >>
> >> The system is made of a pair of proteins in a membrane patch and for
> which
> >> the relative orientation is controlled by non-native
> bond/angles/dihedrals
> >> to perform an umbrella sampling. I use the MARTINI force field but that
> >> might not be relevant here.
> >>
> >> The crashes occur following exchanges that do not seem to occur the
> >> correct way and preceded by pressure scaling warnings … indicative of a
> >> strong destabilisation of the system and eventual explosion. Some
> >> information seems to be exchanged inaccurately.
> >>
> >> Trying to nail down the problem I got stuck and may be some one can
> help.
> >> I placed a pdf file showing plots of bonded/nonbonded energies,
> >> temperatures, box size etc … around an exchange that does not lead to a
> >> crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff
> >> every step with the temperature colour coded as indicated in the first
> >> figure.
> >>
> >> From the figure it appears that the step right after the exchange there
> is
> >> a huge jump of Potential energy coming from the LJ(SR) part of it.
> Although
> >> there are some small discontinuities in the progression of the bond and
> >> angle energy around the exchange they seem to fine. The temperature and
> box
> >> size seem to respond to it a few step latter while the pressure seems
> to be
> >> affected right away but potentially as the Epot will affect the viral
> and
> >> thus the Pressure.
> >>
> >> The other potential clue is that the jumps reduce with the strength of
> the
> >> pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash
> while a
> >> 5/10/20 ps won't. Inspection of the time evolution of the Epot, box …
> >> indicates that the magnitude of the jumps is reduced and the system ca
> >> handle the problem.
> >>
> >> One additional info since I first posted the problem (delayed by the
> file
> >> first attached but now given with a link) the problem is accentuated
> when
> >> the replicas differ in conformation. I am looking at the actual
> differences
> >> as you'll read this email.
> >>
> >> That is as far as I could go. Any suggestion is welcome.
> >>
> >> XAvier.
> >> MD-Group / Univ. of Groningen
> >> The Netherlands--
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