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Thanks Justin for your promt reply, whatever you told is correct, with same .xtc , .tpr , .ndx files I have used in gromacs version 3.3 It is working.<BR>
Thanks alot once again.<BR>
<BR>
>minnale wrote:<BR>
> ><BR>
> ><BR>
> > Thanks to Justin for his suggestion<BR>
> > I tried the way mentioned in http://wiki.gromacs.org/index.php/make_ndx.<BR>
> > I made index file with seperate groups and feed to g_order command<BR>
> > g_order -f .xtc -s .tpr -od scd.xvg -o ord -n .ndx<BR>
> > Group 0 ( C34) has 128 elements<BR>
> > Group 1 ( C36) has 128 elements<BR>
> > Group 2 ( C37) has 128 elements<BR>
> > .<BR>
> > .<BR>
> > .<BR>
> > .<BR>
> > .<BR>
> > .<BR>
> > . and so on till Group 15 ( C50) has 128 elements<BR>
> ><BR>
> > here I am bit confused which group to select , and i selected 1 group?<BR>
> > Is it correct??<BR>
> > Any make me clear about this problem<BR>
> > Thanks in advance.<BR>
> ><BR>
> ><BR>
><BR>
>Which version of Gromacs are you using? I recall some weird behavior from<BR>
>version 3.3.1(?) that I could never get around. Version 3.3, for example,<BR>
>automatically recognizes all the groups in the index file and calculates the<BR>
>order parameters along the chain.<BR>
><BR>
>I don't know if 3.3.1(?) allows you to select multiple groups, but that's what<BR>
>you'd be after - all the groups in the index should be part of the analysis.<BR>
><BR>
>-Justin<BR>
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