[gmx-users] Same values are showing when tried to plot rmsd

[Erik Marklund]

minnale skrev:
>
>  
> Hi all,
> I have run the protein in water for 7ns and plotted RMSD for whole 
> protein with 250 residues and segmented 70 residues out of 250 
> residues by using index file, result in two cases values are nearly 
> same and showing almost same graph. I think it should be different in 
> two cases.
>
> the commands I have given for whole protein and segmented protein are
>
> g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -o rms_whol7nsprot
>   selected c-alpha for least square fit
>   selceted c-alpha for RMSD calculation
>
> g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -n 20_90res.ndx -o 
> rms_segm7nsprot
>   selected 20_90res for least square fit
>   selected c-alpha for RMSD calculation
>
> Any suggestions are appreciated
> Thanks in advance
>
>
>
> Swiss 
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Hi,

You have in fact calculated RMSD for all calphas in both cases, but only 
used a subset of them for fitting in the second case. You need to create 
an index group for the calphas in your segment and use that for your 
calculation (and fitting).

-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys