GROMACS version: 2020.4
GROMACS modification: No
Does anyone know of a simple command to produce a coordinate file of the average coordinates from the MD simulation? Or perhaps a way to produce a coordinate file of a frame from the simulation that is the most representative frame from the entire trajectory?
I am ultimately looking to overlay this representative structure on a PDB file to see if any large structural perturbations have occurred from the introduction of a single amino acid substitution. I wasn’t sure if it would be best to use the average coordinates, representative frame, or final frame from the 200-ns simulation I had run.
Any tips or guidance is appreciated!
I was thinking if you can remove the rotation and translation around the centre of mass of the molecule of interest throughout the trajectory…then you can write a simple ‘awk’ script to find out the average coordinate of each atom. Of course, you need to ensure that the conformation of the molecule has converged.
Are you asking if the RMSD of the mutated protein is converging as in leveling off?
I don’t know if I got your point but …
In order to obtain the most representative conformation of a system you could perform a cluster analysis of the coordinates of your trajectory (gmx cluster)
I suppose you are working with a protein…
Depending on the selection you do, gmx cluster will perform the analysis on coordinates of the whole protein or just on coord. of backbone or C alpha etc…
Be careful because the calculation is heavy, so be sure to not perform it for every ps of simulation…
good luck and let us know!