[gmx-developers] analysis with Amber trajectory files

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 22 13:52:22 CET 2009

Mark Abraham wrote:
> 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.

I have a script that will do such a conversion, available from my website (see 
the email footer).  It hasn't been tested extensively, but it's worked pretty 
well for us in-house.


> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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