[gmx-users] trjconv -pbc

[Andre Farias de Moura]

hello david,

the genconf program worked just fine and I could view my
micelles whole again, thank you.

nonetheless, I've got another related question: the analyses
programs (g_gyrate, for instance) consider those molecules
in the central simulation box or do they apply periodic
boundary conditions and the minimum image convention?

I'm not pretty sure, but it seems to me that it is not
enough to apply PBC and minimum image convention to get
the micelle whole again (this procedure would locate the
images nearer the simulation box origin), and it's not
correct to use those molecules in the central box either.
in both cases, the micellar center of mass and radius of
gyration would not be correct, they would change every
time a lipid molecule jumps across the boundary. is that
right?

I think these programs should find out which molecules are
actually in the aggregate before any structural calculation
is performed... I just don't know how to do it yet.

thanks in advance,

andre


On 9 Mar 2003, David wrote:

> On Sun, 2003-03-09 at 09:58, Andre Farias de Moura wrote:
> >
> > hello rainer,
> >
> > my tpr-file is ok, lipid molecules are not broken after
> > "-pbc whole" option is applied. any other clue?
>
> Since you have a pbc system, lipids will have to be either on one side
> of the box, or on the other. If they move they may be transported to the
> other side. What people usually do for animations of bilayers is to
> extend the pbc (using e.g. genconf)
>
>
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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