[gmx-users] trjconv -pbc

[David]

On Mon, 2003-03-10 at 17:19, Andre Farias de Moura wrote:
> 
> 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.

I have implemented such an option in trjconv:
trjconv -pbc cluster

it is in CVS, but you want to make a separate tree for this, since mdrun
can not be trusted, use it only for trjconv and maybe some analysis
tools (g_cluster, g_clustsize)
> 
> 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++