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

minnale minnale_gnos at rediffmail.com
Mon Jun 2 18:15:24 CEST 2008

Thanks for your prompt reply to Erik and Florian
i have done according to Erik's reply but there is no change in the RMSD values
iam mentioning what i have done

1.make_ndx -f protein.gro -o calpha_re20_90.ndx
 selected 3 & r 20-90 ( 3 = calpha)

this ndx gave input for g_rms 
g_rms -f 7nsprot.xtc -n calpha_re20_90.ndx -pbc -s minwat -o rms_calpha.xvg
  selected calpha_res20-90 for least square fit
  selected calpha for RMSD 
but there is no difference in RMSD values of protein, selected protein&res20-90(index for segment) and calpha&res20-90(suggested one) 

have i made any mistake in mentioning options in commands

Thanks in advance.

On Mon, 02 Jun 2008 Erik Marklund wrote :
>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 <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2133997_2126411/2134144/1?PARTNER=3&OAS_QUERY=null> 
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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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