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.
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.
Hi,
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…