[gmx-users] saving traj of one atom...

[Erik Lindahl]

Giorgos Karvounis wrote:

> Hi,
> I want to run a simulation of , lets say 20 ps, 10000 steps but because
> i'm only interested in the coordinates and velocities of one atom , e.g.
> atom 330 from SOL,
> i dont want to save the rest due to luck of disk space...Is it possible
> to do that?
>
>

Hm.. usually we don't need the velocities (are you sure you do?) for
analysis, so I don't think it's implemented for the .trr files, but for
.xtc trajectories you can just create a group and select that for output in
the .mdp file.

It's close to trivial to implement the same functionality in the .trr
files, but the danger is that these partial files aren't enough to continue
a run since they do not contain all velocities!

Cheers,

Erik