[gmx-developers] Free Format gro File

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 2 09:13:06 CEST 2012

On 2012-10-02 00:59, Jicun Li wrote:
> You are right, Mark. Thank you very much for your suggestions.

I think it is better to adopt another format altogether that is 
supported out of the box by other programs as well.

SDF is such a format:


It would be great to have native SDF support in gromacs.

> Jicun
> 2012/10/1 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
>     On 2/10/2012 8:22 AM, Jicun Li wrote:
>         Maybe the fixed-format gro file is easier to code with in native
>         F77, but it's difficult to prepare with other molecule building
>         software.
>     Sure, but once you've picked a file format, you're stuck with it for
>     a long time.
>         I would like Gromacs to read in the structure exactly, at least
>         as exact as g96 file. But I do not like to use g96 file because
>         there is no atom name in it. I can not use other software to
>         view the structure.
>     There's a separate library of code available on the website for
>     linking to external projects that want to write GROMACS-readable
>     trajectory file formats. That might be useful for you.
>     Wanting to write the atom names in the trajectory file is wasteful
>     if you have a big trajectory. For this reason, tools like GROMACS
>     and VMD can read a structure file and then import a trajectory file
>     that lacks atom information but whose atom ordering matches.
>     You'll be much better off using tools that suit the job at hand:
>     * When you want to view the structure, write a structure file
>     because it has atom names and stuff.
>     * When you want a high-precision trajectory, write a trajectory file
>     because it has high precision.
>     * When you want to view a trajectory, import the latter onto the
>     former. You may wish to reconsider your choice of viewer if you
>     can't do this :-)
>     Mark
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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