Have you checked to see if it is in fact actually moving away, and not
a periodic boundary condition visualisation issue?>

This may help with understanding what is going on ….
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115927.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.



On Thu, 11 Oct 2018 at 20:05, Antonio Carlesso
<antonio.gromacs.carle...@gmail.com> wrote:
>
> 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!
> --
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