[gmx-users] issue in replica exchange

Mark Abraham mark.j.abraham at gmail.com
Thu Apr 25 22:40:53 CEST 2013

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?


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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