[gmx-users] help about "Inconsistent DD boundary staggering limits"

[Justin A. Lemkul]

On 4/26/12 3:30 PM, Desheng Zheng wrote:
> Thanks Justin!
>
> about the "Software inconsistency error: Inconsistent DD boundary staggering
> limits!"
>
> I still have three concerts.
>
> 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5
> environment    with the gro file and top file which were builed under Gromacs
> 4.0.7 ?
>

Coordinate files and topologies are largely independent of version.  There was a 
reorganization of the force fields between 4.0.7 and 4.5, but you can easily 
work around such things.

> 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is
> 0.3V/nm. whether is the value too high to induce the bowling up?
>

I don't know.  The easiest way to deduce the source of the problem is to do so 
scientifically.  Turn off the electric field, does the simulation run? 
Eliminate other factors systematically until you arrive at the root of the problem.

> 3. why do the generated  edr file in gromacs 4.5.5 environment larger than
> the edr file in gromacs 4.0.7 environment, even with the same gro file and
> top file and the same commands?
>

There have been changes to the .edr format and its contents to allow for more 
features.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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