[gmx-users] issue in replica exchange
x.periole at rug.nl
Thu Apr 25 23:05:34 CEST 2013
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? That would explain what I see, but let see what 4.5.7 has to say first.
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?
> On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole <x.periole at rug.nl> wrote:
>> 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
>> 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
>> 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.
>> MD-Group / Univ. of Groningen
>> The Netherlands--
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