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

Dallas Warren dallas.warren at monash.edu
Fri Oct 12 02:17:21 CEST 2018

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 ….

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at 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.carlesso at 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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