[gmx-users] Protein out of the box (not PBC problem)

Carla Jamous carlajamous at gmail.com
Fri Sep 10 11:14:55 CEST 2010

Hi everyone,

please I can't figure out how to do this:

I have a trajectory with water. If I concatenate it, since I have a FAT32
file system, it's a file too large! So I'm trying to avoid this.

For that, I extracted my protein (it's a dimer) from each step of my
simulation (when doing that, I did -pbc nojump and then I fit) and then
concatenated all the steps, to obtain the whole trajectory with only the
protein. When I watch my trajectory with VMD, I suspect that the distance
between the monomers is larger than the dimension of my box.
I'm sure that it's not a PBC problem, because I already did trjconv -pbc
So my question is: is there a way to check if my protein is coming out of
the box, without having to watch the whole trajectory with water molecules,
because I can't do that.

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