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

Simone Orioli simone.orioli at unitn.it
Fri Apr 5 07:41:26 CEST 2019

Hello Neena,

Hello gromacs users,
> Since the final structure obtained after production MD run is the average
> structure,

What do you mean by average structure? The last frame of your MD trajectory
is not an average one, it's the state of your system at the final time of
your simulation.

how to extract out the lowest energy structure?
I'm assuming a free energy is what you're interested in. In that case you
have to answer some questions before doing the actual calculation:
1) what are the relevant collective variables that define your system?
2) do you think your simulation is long enough to accurately sample the
region of conformational space you're interested in? If so, you can project
your trajectory on the space defined by the relevant collective variables
you defined in 1), take -log of it and look for the minima of this
function: this will provide an estimation of the free energy (Helmholtz in
NVT ensemble, Gibbs in NPT ensemble) of your system in units of kBT. Of
course you would have to check for convergence at some point, but this is a
way to start.
If the answer to the question is no, instead, you should consider either
simulating for a longer time or using some enhanced sampling strategy

> Thank you for sharing your knowledge,
> Neena


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