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

minnale minnale_gnos at rediffmail.com
Mon Jun 2 12:40:04 CEST 2008

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
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