[gmx-developers] analysis with Amber trajectory files

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 22 13:03:04 CET 2009

oguz gurbulak wrote:
> Dear All,
> I'm planning to use Gromacs 3.3.3 for analysis with Amber trajectory 
> files ( mdcrd, rst files ). And I searched the mail archive about this. 
> I learned that I can use trajconv to convert  Amber trajectory files to 
> Gromacs format. But I think I should also convert units ( angs to nm ). 
> How can I successfully convert units ? and Are there any operations I 
> should do apart from these ?

This is a question more about GROMACS usage than GROMACS development, 
and so belongs on the GROMACS users mailing list.

The trjconv documentation doesn't say it will convert AMBER trajectory 
formats to others, and it would be inconsistent for it to be the only 
GROMACS tool that does. I think you will need to do this operation in 
two stages via some intermediate format, like PDB. All GROMACS utilities 
could just read such a PDB trajectory, but the file would be much larger 
than it needed to be. You will not need to worry about unit conversion - 
they're implied by all the file formats and all the GROMACS tools will 
get it right.


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