Hello everyone, I am trying to evaluate the convergence of protein structure during simulation to equilibrium state with "gmx rms", however I see strange (to me) results when RMSD goes from high in the beginning of simulation to low in the end of simulation - I would expect the trend to be opposite.
System: Small 37 aa protein interacting with infinite slab of polymer surface. RMSD calculation: echo 4 4 | gmx rms -f trjconv_processed_results.trr -s beginning-structure-nowater.gro -o rms-backbone-start.xvg where: "trjconv_processed_results.trr" = post-simulation .trr with water removed and system made "whole" by successive trjconv runs with -pbc flags: -pbc whole --> -pbc nojump --> -pbc mol "beginning-structure-nowater.gro " = .gro without water used to setup .tpr of the simulation analyzed Problem: The RMSD trend goes from high to low, which is different to what I would expect - shouldn't it go from 0, up to some point and then hopefully equilibrate? The visual inspection of output simulation .pdb files shows very clear deviation from the shape of original structure as protein binds to the polymer surface. The RMSD calculations of 5 independent simulations of the same system (staring with different velocities/configurations) can be seen at the link below: https://www.dropbox.com/s/gmo61ah6txu6pty/Untitled1.png?dl=0 Question: Am I doing something wrong with "gmx rms" command? Or such output is expected and my expectations are wrong? Thanks in advance! Wei-Ta Li -- 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.