[gmx-users] Re: Problem calculating RMSD with gromos

Melchor S. msmqbm at cid.csic.es
Tue Jul 2 15:37:32 CEST 2013

I expected to see how the RMSD increases with time respect the closed
cristallographic structure and decreases with time respect to the open
crystal structure.

I obtained it for OPLS, but with gromos I obtain a kind of mixture in that
you see that the structure behaves different between the open ad close
conformations at the beginning  but then remain at thesame distance.  You
don't see a clear differenciation between the closed and the open forms. And
you have to see it. 

Forn calculate I used g_rmsd -d traj.trr -s Crystal_structure.gro -o
rmsd.xvg I do it over the backbone

Also, I visualize it in VMD, loading the gro  and the trr files, and the the
crystal structures. Using the Trajectory  analysis tool , I align the
strucutres and calculate the RMSD over the crystal structure.

Something easy, not problematic in principle, but is giving me a lor of
problems with gromos, because I have repeated three times the simulation,
obtaining similar pictures as the one that you can see below.

I want to know if there is some reason for this behaviour or not, Maybe you
need more time to equilibrate with gromos than with OPLS?

For the initial setup of the simulation, I follow the same procedure in all
cases with the same settings, I even added manually the protonation states
of the terminal residues and also of the Histidines.




Melchor S.

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