[gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

[John Degenstein]

Hello,

I am trying to build a bigger liquid phase (1000) from a small cluster of
molecules (125). So far I have succeeded in forming the small cluster of
125 molecules shown in the below image. This was after running gmx trjconv
... -pbc cluster -center to bring the molecules into the middle of the box.

http://i.imgur.com/nlgDUzh.png

Now, the seemingly very trivial issue I am having is that I cannot figure
out how to remove the empty space surrounding the cluster. I would like to
do this automatically rather than by manually specifying a box size. Can
anyone suggest a workflow for doing this?

Thanks,
John