[gmx-users] VMD and trajectory files

[Ilya Chorny]

I'm not exactly sure what the advantage is to using the xtc vs trr. I
think both will work. I believe the trr output can be adjusted by
setting nstxout = 100. The trr files contains more info then just
coordinates like velocities and forces.

-x option in mdrun directs the output to a file name for the .xtc
output.

type mdrun -h for more info 

Ilya


 
On Thu, 2003-11-20 at 16:27, Derrick Guang Yuh Lee wrote:
> dear Ilya
> 
> thank you for the info, two things though. is there any advantage of
> having VMD use the xtc file over the tjr file? and you mentioned the -x
> option of mdrun, i'm not a hundred percent sure what you mean by that,
> could you please be a bit more detailed about that? thanks.
> 
> 
>  - derrick
> 
> 
>  derrick Lee
>  faculty of Science
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca or derrickglee at hotmail.com
> 
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst."
>                                                               - bruce lee
> 
> On Thu, 20 Nov 2003, Ilya Chorny wrote:
> 
> > VMD can read xtc files as well. VMD reads the corrdinates it doesn't
> > need velocities.
> >
> > Set
> >
> > nstxtcout = 100
> >
> > and don't forget the -x option in mdrun
> >
> > Ilya
> >
> >
> > On Thu, 2003-11-20 at 15:40, Derrick Guang Yuh Lee wrote:
> > > dear [gmx-users]
> > >
> > > i was just curious if someone could help me create a movie for VMD. it had
> > > just occured to me that i can use my trajectory file (.tjr) to view my
> > > monolayer in VMD, but because it is 1ns simulation, the file is a little
> > > too large for VMD and our computers here.
> > >
> > > so, would anyone be able to inform me of how i could set it up such that
> > > my trajectory file prints out the velocities and coordinates of my system
> > > about 100 times or so? it'd be appreciated. thanks.
> > >
> > >
> > >  - derrick
> > >
> > >  derrick Lee
> > >  faculty of Science
> > >  Memorial University of Newfoundland
> > >  k24dgyl at mun.ca or derrickglee at hotmail.com
> > >
> > > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > > truth that each student must find for himself. a good teacher is merely a
> > > catalyst."
> > >                                                               - bruce lee
> > >
> > > _______________________________________________
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> > --
> > ----------------------------------------------------------------
> > Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
> > Postdoctoral Researcher   University of California-San Francisco
> > phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
> > fax: (415)502-1411        San Francisco, Ca, 94107
> >             email: ichorny at maxwell.ucsf.edu
> > ----------------------------------------------------------------
> >
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