[gmx-users] RMSD, two simulations

Marcus Kubitzki mkubitz at gwdg.de
Thu Jun 26 13:56:01 CEST 2008

Hi Michael,

g_rms should do the trick. First create an index file having
an atom group identical in both systems. Then,
g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives
you an rmsd matrix with entry ij given by
RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that
matrix should be what you want.


Michal Kolinski wrote:
> Dear Users,
> I've created two different models of the same
> transmembrane protein.  These two models were
> created using homology approach using two different
> templates (both with similar sequence similarity
> to the sequence of the target protein).  Next, I
> did two separate 25ns simulations of those two
> obtained protein models in water and lipid environment. 
> RMSD value calculated using g_rms reaches about 3.5 A
> after 10 ns in two simulations and stays stable for
> the rest of the MD time. 
> What I want to do is to obtain a plot  of  RMSD
> between those two models (model one vs model two)
> for each corresponding frame of those two MD simulations
>  (I just want to add that the length of protein chain is
> different in both protein models).    Is there a script
> available from gromacs tools which could be used for this? 
> Could you give me some sugestions how to treat this problem?
> Thank you in advance.
> Michal
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Dr. Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
phone: ++49-551-2012312
fax: ++49-551-2012302
Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/

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