[gmx-users] viewing the trajectory

Erik Lindahl lindahl at stanford.edu
Sat Jun 7 01:59:01 CEST 2003

On Friday, June 6, 2003, at 12:36  PM, Vivek Raut wrote:

> i have a .trr & .edr file.
> i want to see the trajectory running. how do i do that?

You will need the .tpr file too, since that contains all information 
about atom names, bonds, etc. (trr is only coordinate values, no names 
to save space).

You can use the simple/ugly built-in program ngmx in gromacs, or VMD, 
gOpenMol, etc. You can also convert the file to pdb with trjconv and 
use Pymol. Pymol will get native gromacs support in the future...

> also from the .trr file i want to track the z- coordinate of a 
> particular molecule. how do i do that?

use g_traj ("g_traj -h" or "man g_traj" or see the manual for help)

You can define an index group if you only want to extract coordinates 
for a subset of atoms.



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