[gmx-developers] analysis with Amber trajectory files

[Justin A. Lemkul]

oguz gurbulak wrote:
> Dear Justin,
>  
> First of all, I want to thank you for your attention. I got the script 
> and I will definitely use it for my study. I'm also an Amber user. Amber 
> mostly products a mdout, a mdcrd an a rst file at the end of a md. 
> Should I also convert the rst file that includes last coordinates of the 
> system and use this  in Gromacs ? What do you thing about that ? Because 
> I'm new to Gromacs and want to learn the accurate procedure. And Does 
> Gromacs convert the angs to nm by itself ?
>  

What you use for analysis is really dependent upon the type of analysis you want 
to conduct.  There is nothing special about how you analyze your results, just 
because you are using Gromacs.  How would you analyze a trajectory under Amber?

Gromacs can use .pdb files as input, so conversion of A -> nm is really superfluous.

I agree with Mark, further discussion really belongs on gmx-users, since that is 
the point of that listserv, and you will reach a wider audience of users who may 
be doing some of the same things.

-Justin

> Sincerely
> 
> --- On *Sun, 2/22/09, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-developers] analysis with Amber trajectory files
>     To: "Discussion list for GROMACS development"
>     <gmx-developers at gromacs.org>
>     Date: Sunday, February 22, 2009, 6:52 AM
> 
>     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.
> 
>     -Justin
> 
>     > 
>     > 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
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================