[gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 10 12:05:09 CEST 2010

Hi Nahren,

You can do that using trjconv and an index file with the atom indices as
they are in the order as they have to be.

But is that really your problem? To understand what happened, it would help
if you gave the series of commands that led to these results.



On Mon, May 10, 2010 at 11:42 AM, nahren manuel <meetnahren at yahoo.com>wrote:

> Dear Gromacs Users,
> I simulated two homologous (proteins) , and noticed after the simulation
> that in one trajectory, the protein is stored as ABCXYZ and in another it is
> as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ is
> another trimer, so the system is a trimer-trimer complex)
>  I should not have any issues for most of my trajectory analysis. But when
> I wanted to get a correlation plots of the CA-CA from the covariance matrix,
> the plots cannot be compared, as the information in the trajectory is
> different.
>  So is there a way that I can convert my trajectory from ABCXYZ to AXBYCZ.
>  Thank you,
> nahren
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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