[gmx-users] How to determine box shape and parameters from a run

[Tsjerk Wassenaar]

Hi Ramon,

That's a rhombic dodecahedron with a square XY base.

Cheers,

Tsjerk

On Tue, Nov 3, 2015 at 5:12 PM, Ramon Crehuet <rcsqtc at iqac.csic.es> wrote:

> Thanks Justin,
> The edr file is binary and I don't know how to access it.
> I had seen that the gro file contains the vectors, and the documentation
> says the following:
>
> * box vectors (free format, space separated reals), values: v1(x) v2(y)
> v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)*
>
> However I still don't know what these components are and how to relate
> that to a dodecahedron, truncated octahedron, etc.
> In particular, my file contains:
>
>   13.27362  13.27362   9.38587   0.00000   0.00000   0.00000   0.00000
> 6.63682   6.63682
>
> Thanks again,
> Ramon
>
>
> On 11/3/15 5:56 AM, Ramon Crehuet wrote:
> >* Dear all,
> *>* This is a very simple question, but I could not find the answer in the
> *>* documentation. Some time ago I run a simulation and now I don't remember the box
> *>* shape and sizes I used. In which file is this information contained?
> *>* A related question is whether the box volume is printed somewhere or I need to
> *>* calculate it from the parameters.
> *>* Thanks in advance,
> *>* Ramon
> *>>* PS. My log contains Box-X Box-Y and Box-Z parameters. Does that mean I used a
> *>* rectangular box?
> *>
> Box vectors are stored in the .edr file, and you can verify the shape from the
> vectors printed to any coordinate file (your starting coordinates, dumped from
> the .tpr if needed, or any final coordinate file printed by mdrun).
>
> -Justin
>
>
> --
> Ramon Crehuet
> Cientific Titular (Assistant Professor)
> Institute of Advanced Chemistry of Catalonia
> IQAC - CSIChttp://www.iqac.csic.es/qteor https://twitter.com/rcrehuethttp://ramoncrehuet.wordpress.com/
> Tel. +34 934006116
> Jordi Girona 18-26
> 08034 Barcelona (Spain)
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.