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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
