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 nojump. 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. Thanks, Carla
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