[gmx-users] ngmx

[David van der Spoel]

On Wed, 2004-01-07 at 16:43, Osmany Guirola Cruz wrote:
> I do a grompp to my tpr file with the flag -deshuf
> and then do a trjcon to my .trr file with the deshuf.ndx
> and does not work

check the archives for deshuffling. it's a pain I'm sorry to say, but it
can be done.

> 
> 
> On Wed, 2004-01-07 at 09:38, Nuno R. L. Ferreira wrote:
> > Hi Osmany
> > 
> > Grompp writes an index file with flag -deshuf.
> > Then, use trjconv to deshuffle your traj.
> > Regards
> > Nuno
> > 
> > 
> > ######################################
> > Nuno Ricardo Santos Loureiro da Silva Ferreira
> > Departamento de Química
> > Faculdade de Ciências e Tecnologia
> > Universidade de Coimbra
> > 3004-535 Coimbra - Portugal
> > Fax: +351 239 827703  - www.biolchem.qui.uc.pt
> > ########################################
> > ----- Original Message ----- 
> > From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
> > To: <gmx-users at gromacs.org>
> > Sent: Wednesday, January 07, 2004 2:07 PM
> > Subject: RE: [gmx-users] ngmx
> > 
> > 
> > > yes i am using shuffling in my simulation in my cluster i am usin 8
> > > machines .
> > > What can i do to see my simualtion .?
> > > eliminate the shuffling option?
> > > or exist another way to see the simulation
> > >
> > >
> > >
> > > On Wed, 2004-01-07 at 08:46, David van der Spoel wrote:
> > > > On Wed, 2004-01-07 at 14:23, Osmany Guirola Cruz wrote:
> > > > > First I load my .gro file whitout problem but when I load the .trr
> > file
> > > > > to see the simulation
> > > > > VMD begins to draw my protein very bad ... It joins atoms that are not
> > > > > joined before load the trr file.
> > > > > These ocurrs in many of the atoms of my system
> > > > >
> > > > does your trr file correspond to the gro file, i.e. is the order of
> > > > atoms the same?
> > > > It will not be the same when you have used shuffling for your simulation
> > > > (on parallel computer)
> > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: David [mailto:spoel at xray.bmc.uu.se]
> > > > > Sent: Tuesday, January 06, 2004 3:53 AM
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: Re: [gmx-users] ngmx
> > > > >
> > > > >
> > > > > On Mon, 2004-01-05 at 16:44, Osmany Guirola Cruz wrote:
> > > > > > I need to know if exist another tool to visualizate
> > > > > > Trr files I think that ngmx is not the best. I use VMD but it give
> > me
> > > > > > errors drawing  my molecules whith the trajectorie files  , I need
> > use
> > > > >
> > > > > > other tool.
> > > > >
> > > > > What kind of errors, VMD works reasonably well for most gromacs
> > users...
> > > > >
> > > > > >   WHICH?
> > > > > >
> > > > > > _______________________________________________
> > > > > > 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.
> > >
> > >
> > 
> > 
> > _______________________________________________
> > 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.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++