[gmx-users] g_RMS

[David]

 On Tue, 2005-10-25 at 14:36 +0200, Michal Kolinski wrote:
> Hi all
> 
> I used g_rms  to calculate RMSD for peptide ligand (inside receptor
> active site) for 2 ns simulation.  I don’t understand why are the
> obtained values for RMSD so high (are the units nm, or A)?   From the
> trajectory it looks like  ligand is very  stable.  

Your file is suspicious. It contains comma's in stead of decimal points.

Numbers are in nm.
> 
> Thank you in advance.
> 
> Michal    
> 
>  
> 
>  
> 
> My g_rmsd output:…
> 
> #          This      file        was      created by
> g_rms_mpi                                                      
> 
> #          which   is          part      of         G         R
> O         M        A         C         S:
> 
> #          Gravel  Rubs    Often   Many   Awfully
> Cauterized       Sores                                      
> 
> #          All        this       happened         at:        Tue
> Oct      25        13:51:37          2005                
> 
> #                                                                                                                               
> 
> @        title
> RMSD                                                                                               
> 
> @        xaxis    label     Time
> (ps)                                                                                           
> 
> @        yaxis    label     RMSD
> (nm)                                                                                       
> 
> @TYPE
> xy                                                                                                                  
> 
> @        subtitle DAM after lsq fit to
> DAM                                                                                                     
> 
> 0
> 0,0002                                                                                                           
> 
> 2
> 1,8792                                                                                                           
> 
> 4
> 1,3783                                                                                                           
> 
> 6
> 1,3538                                                                                                           
> 
> 8
> 2,0421                                                                                                           
> 
> 10
> 2,0478                                                                                                           
> 
> 12        2,0536
> 
> 14        2,4779
> 
> 16        2,4665
> 
> 18        3,1466
> 
> 20        2,642
> 
> 22        2,6397
> 
> 24        2,9798
> 
> 26        4,1681
> 
> 28        2,9859
> 
> 30        2,9585
> 
> 32        3,2852
> 
> 34        3,2984
> 
> 36        3,2861
> 
> 38        4,0952 …..
> 
> …
> 
> …
> 
> ..
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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