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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Jun 2 13:05:21 CEST 2008


On Monday, 2. June 2008 12:40, minnale wrote:
> 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

This could be a normal behaviour, the rmsd fluctuations depends on several 
factors, for example function of the protein (closing and opening from 
flaps ..) and so on.

Also the timescale is not really long.

You can also take a look at a RMSF plot of your simulation, and see which 
parts of the protein shows the largest fluctations.

> Thanks in advance



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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