[gmx-developers] Free Format gro File

[Mark Abraham]

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