[gmx-users] Re: making index file (old topic)

Pim Schravendijk schraven at mpip-mainz.mpg.de
Tue Jun 15 11:45:49 CEST 2004

Sorry for bringin up an old problem, but there was no answer to the
question below yet, and I just happened to make the same mistake and find 
the answer as well.

Selecting group x & group y means that a new group will be made consisting 
of the parts that are present in _both_ group x and group y. This will not 
combine the two groups! If one justs wants to combine two groups the OR 
command has to be used.

What goes wrong here is that you should think about it as a programmer, 
not as a human ;)

Tschuess, Pim

> --__--__--
> Message: 6
> Date: Wed, 14 Jan 2004 18:00:36 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry
> To:  gmx-users at gromacs.org
> Subject: Re: [gmx-users] making index file
> Reply-To: gmx-users at gromacs.org
> Zhu, Qing wrote:
> > Dear gmx-users:
> >      I ran MD simulations on a hexameric bundle of Alm helices in a
> >      POPC bilayer. After 1-ns simulation I created an index group made
> >      up of some lipids, but I cannot make such index file using the
> >      same residue numbers after 10-ns simulation(the only difference
> >      is the simulation time length and the system told me "Group is
> >      empty"). It seems so odd that I am very confused. Any helpul
> >      suggestions would be greatly appreciated.
> Are you using shuffle and/or sort (grompp options that change the order
> of molecules in your system)?
> -- 
> Groetjes,
> Anton

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