David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 7 14:57:01 CET 2004
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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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
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