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. Cheers, Tsjerk On Mon, May 10, 2010 at 11:42 AM, nahren manuel <meetnah...@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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
