[gmx-users] fatal error in g_order

[Justin A. Lemkul]

Follow the message that you found in the archive.  The index file must specify
each carbon atom type in separate groups (a group for all C12, a group for all
C13, etc), and the index file must contain *only* those groups, as I told you
before.  If you check the output from g_order, you'll see that it is trying to
involve 'System,' 'SOL,' etc. in the calculation.  That should be a clue that
something is going very wrong.

-Justin

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
> I had made groups using make_ndx command and selected say "a C12|a C13....."
> and named one group as palmitoyl and other group as oleoyl but when I select
> these groups during the execution of commamd  get the error:
> > > Groupname: System First atomname: C1 First atomnr 0> > Groupname: POPC
> First atomname: C1 First atomnr 0> > Groupname: SOL First atomname: OW First
> atomnr 6656> > Groupname: oleoyl First atomname: C1 First atomnr 1820> >
> Groupname: palmitoyl First atomname: C1 First atomnr 832> >> > Reading frame
> 0 time 0.000 Number of elements in first group:> > 14036> >
> -------------------------------------------------------> > Program g_order,
> VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> >
> grp 1 does not have same number of elements as grp 1
>
> Is there something I am doing wrong? something I dont know of while using
> g_oder. I have read the mailing list and made groups accordingly.
> One more question: In the mailing list it was wriiten to make separate group
> for CH3, CH2,CH. Is that the mistake I am doing since I am specifying the
> whole chain. > Date: Sun, 3 Feb 2008 12:38:43 -0500> From: jalemkul at vt.edu>
> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] fatal error in g_order> >
> > This issue is well-documented in the list archives. You need to create an
> index> group that specifies *only* the groups of interest in the index file,
> i.e. C16,> C17...> > There is a post (I believe from Dallas Warren) that even
> gives examples of> make_ndx commands to create such groups, if you need that
> kind of help.> > -Justin> > Quoting pragya chohan
> <pragyachohan at hotmail.com>:> > >> > hi> > I am trying to do the bilayer
> analysis and want to calculate order parameters> > using g_order. I made the
> index using make_ndx command and selected the> > carbons sai 1-16 of my first
> chain and 17-33 of the other in same index file> > as two separate group.
> When I am giving this index file to g_order I get the> > error:> >> > Using
> following groups:> > Groupname: System First atomname: C1 First atomnr 0> >
> Groupname: POPC First atomname: C1 First atomnr 0> > Groupname: SOL First
> atomname: OW First atomnr 6656> > Groupname: oleoyl First atomname: C1 First
> atomnr 1820> > Groupname: palmitoyl First atomname: C1 First atomnr 832> >> >
> Reading frame 0 time 0.000 Number of elements in first group:> > 14036> >
> -------------------------------------------------------> > Program g_order,
> VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> >
> grp 1 does not have same number of elements as grp 1> >> > Please help.> >> >
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> ========================================> > Justin A. Lemkul> Graduate
> Research Assistant> Department of Biochemistry> Virginia Tech> Blacksburg,
> VA> jalemkul at vt.edu | (540) 231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> >
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================