[gmx-users] gmx rms divergence from the starting structure

[Wei-Ta Li]

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