[gmx-developers] Free Format gro File
Mark.Abraham at anu.edu.au
Tue Oct 2 00:54:55 CEST 2012
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
> 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 :-)
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