[gmx-users] RMSD for domain

Xavier Periole x.periole at rug.nl
Mon Jul 17 18:12:10 CEST 2006

> My protein consist of two domains.
> I got RMSD plot for complete system.
> According to the manual one can calculate RMSD for different time 
> period by initiating initial and final time.
> Will it be possible to calculate RMSD for two seperate domains(by 
> restricting residues) of the same system over same time period?

Yes, you have to generate an index using make_ndx -f protein.gro(pdb)

the use g_rms -f traj.trr(xtc) -n index.ndx and the program asks you to 
a group in the index for the least square fit and for the rmsd 
calculation. You
just have to make your choice.


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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