[gmx-users] Re: gmx-users Digest, Vol 52, Issue 5

[minnale]

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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