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