[gmx-users] how to generate average structure from trajectory

[Sadaf Rani]

Dear Subhomoi
Thanks for your reply.
I was doing the following:-
discarding 1 ns trajectory by the following command:-
gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o
md_1000ps.xtc

Extracting average structure by the following command:-

gmx rmsf -s md.tpr -f md_1000ps.xtc  -o rmsf1000ps.xvg -ox
average1000ps.pdb  -res -n index.ndx
I am confused between using gmx rmsf and gmx cluster for getting average
structure

for clustering should I do the following?
gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb

Can you please correct me.

Thanks in advance.

Sadaf