[gmx-users] ngmx

[Osmany Guirola Cruz]

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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