[gmx-users] particle decomposition with distance restraints

[Da-Wei Li]

Dear Mark

Here it is some information that may be useful. I checked all my -pd, with
distance restraints MD runs. It seemed that crash usually happened when
protons and the carbon they attached were in different processors.

best,

dawei


On Thu, Dec 13, 2012 at 4:12 PM, Da-Wei Li <lidawei at gmail.com> wrote:

> 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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