[gmx-users] ngmx

[Nuno R. L. Ferreira]

What about your pbc treatment? Try -pbc whole with -n reading your deshuffle
index file.
And, check e-mail .
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
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----- Original Message ----- 
From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
To: <gmx-users at gromacs.org>
Sent: Wednesday, January 07, 2004 3:43 PM
Subject: Re: [gmx-users] ngmx


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


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 QuÃf­mica
> Faculdade de CiÃfªncias 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?
> > > > >
> > > > > _______________________________________________
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>
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