[gmx-users] particle decomposition with distance restraints

[Mark Abraham]

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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