[gmx-users] Lowest energy structure after production MD run

Dallas Warren dallas.warren at monash.edu
Fri Apr 5 04:46:29 CEST 2019

The final structure at the end of a production MD is actually simply the
structure of the system at that moment in simulation time. You need to
analyse the system over the appropriate trajectory time frame to gain the
information you are looking for.

Check http://manual.gromacs.org/current/reference-manual/analysis.html to
see what is available within GROMACS that might be appropriate. If you
can't find what you want there, then there are other MDS analysis packages

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

On Fri, 5 Apr 2019 at 13:23, Neena Susan Eappen <
neena.susaneappen at mail.utoronto.ca> wrote:

> Hello gromacs users,
> Since the final structure obtained after production MD run is the average
> structure, how to extract out the lowest energy structure?
> Thank you for sharing your knowledge,
> Neena
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