[gmx-users] re-imaging plus distance analysis problem

[Antonio Carlesso]

Hi all,

we have some problem in correctly reimaging a protein-multiple ligands MD
simulations.

Since we were trying in investigating the recognition process some ligands
“fly away” from the binding region and going out from the box (10 Å length).

When calculating the distance over time between two pair of atoms using gmx
distance the analysis does not match with the value obtained in VMD and
with snaphots downloaded every 100 ns..





Do you have any idea how to fix this issue?

Thank you!