[gmx-users] particle decomposition with distance restraints

[Da-Wei Li]

Dear Mark

Thanks for the quick response. This has bothered me for some time. I feel
something is wrong because

1. If I turn off lincs (dt will be 0.001 instead of 0.002 ), I can run the
same simulation for very long (>500 ns) without any problem. By saying
"same simulation", I mean everything is identical except dt (=0.001) and
constraints (= none). Once I turned on lincs  (even with dt is still 0.001)
by set constraints to hbonds, the md run will crash from time to time.

2. With the help of cpt file (it is a numerical exact re-start because I
don't change anything and I use the same number of processors), I usually
can pass the last time crash point without error.

best,

dawei


On Thu, Dec 13, 2012 at 12:17 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 1) AFAIK there are indeed conditions under which domain decomposition does
> not work with distance restraints
> 2) Your symptoms could just be that (some of) your initial conditions, or
> them in combination with the restraints are problematic. Without more
> description about why and how you're using the restraints, and that your
> systems are stable in the absence of restraints, it's hard to say much.
> 3) Generally, turning off the restraints is not a proper solution (and
> particularly not without adjusting the time step accordingly) - see
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 4) We're a long way from supposing there's a code bug :-)
>
> Mark
>
> On Thu, Dec 13, 2012 at 4:40 PM, Da-Wei Li <lidawei at gmail.com> wrote:
>
> > Dear Gromacs users
> >
> > I recently tried distance restraints simulation and  I have been forced
> to
> > use -PD (particle decomposition) because domain decomposition doesn't
> work
> > with distance restraints. However, my MD run will crash randomly for some
> > of my proteins but works well for others. Once it is crashes, I try to
> > rescue it by restart it using CPT file. Some times, the simulation can
> pass
> > the crash point and continue for a long time and some times it just keep
> > crashing. The only work-around I found is to turn off lincs. Does this
> mean
> > a bug in the code? I observed this for 4.5 and 4.6.
> >
> > best,
> >
> > dawei
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