How to select the best representative conformation with the lowest energy using gromacs?

User discussions
1

GROMACS version: 2020.4

After finishing my simulation of my peptide with 200ns , how to select the best representative conformation with the lowest energy using gromacs ?

2

Hi Sam,

gmx energy helps you to find the timeframe with the lowest energy.

If you need a really low energy configuration, I suggest you run additional annealing runs where you lower the temperature to zero, starting from multiple different frames in your simulation.

3

thanks for replying , Do you mean that i can use the output data of potential energy to find the lowest energy conformation ?

4

Hi Sam,

Yes! When you run gmx energy and then select the potential energy, you will get an xvg file. From this file you can determine the time-frame with the lowest potential energy.

5

thanks for replying and helping … i will do it

6

Note that the lowest potential energy is not the lowest free energy, and moreover force fields are not designed in such a way that these system potential energies are in any way physically meaningful.