[gmx-users] gmx genconf

[Christian Blau]

Hi Alex,


It's not possible with genconf. genconf only ever outputs a single 
structure. If you provide a trajectory, each frame in the trajectory is 
matched with a grid position that is then output as a single structure.

If you're looking into this for the sake of visualisation, tools like 
vmd and pymol usually do provide the functionality to generate periodic 
images. If you're after some analysis, it's often better to make use of 
the symmetry properties in the analysis explicitly rather than doubling 
the data.


Best,

Christian

On 2020-01-15 19:10, Alex wrote:
> Dear all,
> I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
> order to expand a gro file 2 times in all directions. I wonder if it is
> possible to expand a xtc trajectory and outpout a larger trajectory in the
> same way?
>
> According to genconf man page I see that the input could be -trj.xtc, but
> no trajectory as output has been mentioned there apparently.
>
> Regards,
> Alex