[gmx-users] RMSD, two simulations

Michal Kolinski mkolin at iimcb.gov.pl
Thu Jun 26 13:38:30 CEST 2008

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.
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