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

Erik Marklund erikm at xray.bmc.uu.se
Mon Jun 2 13:09:03 CEST 2008

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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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

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