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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 2 16:24:27 CEST 2013

Hi Melchor,

Have you looked at the structures? The GROMOS people suggest using
twin-range cut-off with reaction field correction, and the Vanderwaals
cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS.
Maybe that makes a difference.



On Tue, Jul 2, 2013 at 3:37 PM, Melchor S. <msmqbm at cid.csic.es> wrote:

> 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.
> <http://gromacs.5086.x6.nabble.com/file/n5009497/OPLS2.png>
> Gromos
> <http://gromacs.5086.x6.nabble.com/file/n5009497/Gromos.png>
> cheers,
> Melchor S.
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Tsjerk A. Wassenaar, Ph.D.

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