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

[Anton Feenstra]

Erik Lindahl wrote:
> 
> 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!

It also sounds like you (Giorgos) are going to store a frame each time
step. In that case I would say the velocity is obsolete (you can get it
back from the difference between subsequent positions, obviously), so
you could simply use the xtcgroups option.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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