GROMACS modification: No
I tried to calculate the average structure of my system (125 molecules of an organic molecule) using dcovar tool (See below for the command) but the resulted average structure was blown up with many unusual bonds. Can someone help me on this?
gmx dcovar –f traj.xtc –s topol.tpr –b 801 –e 1000 –av .pdb
When you calculate an average structure, it is a ‘geometrical’ average, meaning that the result does not have to be (and usually is not) physically relevant (that is why your bond lengths are wrong, and thus are represented in a very weird way).
Think of the following example: You have a pendulum, and you have a simulation of it swinging from left to right along a curve. If you take the average of the most-left and most-right configurations, the average structure will be in the middle, but higher than the resting position of the pendulum: the average structure corresponds to a configuration that your simulation cannot reach!
If you want to find a representative structure of the trajectory, try with the
gmx cluster module
Thank you for the detailed explanation. I used the cluster module to generate a representation of the largest cluster.