[gmx-users] How to get the correct reference frame to run the rmsf?

[ZHANG Cheng]

Dear Gromacs,
I try to use this command to calculate RMSF:


echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq bfac.pdb -res -b 20000 -e 30000


My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is mandatory to assign a reference frame, so I use "md_0_1.tpr", which gives the frame at time 0 ns.


However, I think I should use a frame which is a time-averaged position within 20-30 ns. Can I ask how to get this frame?


In addition, the command line outputs a PDB file. So what does this conformation represents, time 0, 20 or 30 ns?


Thank you.


Yours sincerely
Cheng