[gmx-developers] Free Format gro File

Jicun Li jerkwin at gmail.com
Tue Oct 2 00:59:47 CEST 2012

You are right, Mark. Thank you very much for your suggestions.


2012/10/1 Mark Abraham <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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