[gmx-developers] extraction of trj files

[Mark Abraham]

Dave Segala wrote:
> To Gromacs Developers:
> 
>    I have simulated my protein and have my trajectory file with both
> position and velocity for each atom. What I am trying to do is take
> those positions and velocities and store them into their own
> arrays/matrices as a matfile (matlab file). The way I am doing this
> seems to be not the right or best way. I redirect the output of the trj
> using gmxdump to a text file (gmxdump -f file.trj > file.txt). The trj
> file is 8GB and the text file is 30GB.
>   Is there anyone that can give me the structure of the trj file(I know
> its binary) to bypass the text file? Does anyone have a better way of
> extracting the pos and vel into matlab arrays/matrices.

Check out http://wiki.gromacs.org/index.php/Using_Trajectory_Information 
for some ideas here.

Mark