[gmx-users] Non Periodic Coordinate File

[ANAND AMITKUMAR Dharia]

Hello,

I was wondering if it was possible to create a non-periodic coordinate file
using trjconv or some other gromacs program on a trajectory file. I would
like to use coordinate data to calculate displacement in order to compute a
crosscorrelation between molecules, however, with the jumps in the
coordinate file, there is no meaningful result. I understand I can use the
-ur pbc mol command, but this just makes the molecule whole before bouncing
across the screen. Any input would be helpful.

Thanks,
Anand