[gmx-users] Calculating avergae structure from the simulation

[Agnivo Gosai]

Dear Users

I had run an unrestrained 50 ns simulation of a protein-ligand complex
using GROMACS to check the stability of the force field used and compare
with previous literaure.

Then I dumped the strucuture from the last frame of the 50 ns simulation
and used it for pulling and umbrella sampling simulations.

Now, the reviewer is asking me this "Reference structure should have been
the average structure, not the final state seen at the end of 50 ns MD run.
"

Is there any tool in GROMACS by which I can calculate the average structure
?? I was thinking that this is a normal procedure to conduct the
simulations.But now I am confused. Kindly comment.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.