[gmx-users] Same values are showing when tried to plot rmsd
minnale_gnos at rediffmail.com
Mon Jun 2 12:40:04 CEST 2008
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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