[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck

[Justin Lemkul]

On 3/10/15 8:54 AM, gromacs query wrote:
>>> You can probably confirm that from the time series of some observables.
>
> In the end of log file it complains about these two atoms:
>
> the first 10 missing interactions, except for exclusions:
>                  Bond atoms   94  177           global    94   177
>                  Bond atoms   97  177           global    97   177
>
>
> I checked these two atoms and visually they look fine and whole system
> behaves nicely. I am not sure, what observables I can measure?
>
> I restarted the job its running without error. I got this error when
> protein was in edge of the box though in PBC it makes no sense to say like
> that.
>

Coincidence, nothing more.  The issue is that CG bonded interactions occur over 
longer distances than are typical in atomistic simulations.  For that reason, 
you need to tune DD cell size more specifically, by using -rdd and whatever 
other options there are.  There have been discussions on this in the past.

> I have one silly query, why always in such cases when I simulate something
> with membrane my protein loves to stay always in the edge of box? I mean,
> If you visualise in VMD non-imaged trajectory. (Though I understand in PBC
> there is no edge).
>

Probably incidental.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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