[gmx-users] losing data in trjconv?

[Lucio Ricardo Montero Valenzuela]

Hello,
you have to use the -force parameter in trjconv, to copy also the forces
in the original trr file.
Best regards
Lucio

El lun, 15-10-2012 a las 21:18 +0800, Gil Claudio escribió:
> Hi Justin,
> 
> My original intention was to lessen the 5 ns trajectory to transfer to another drive. I did
> 
> trjconv -f traj.trr -o traj_1.trr -b 0 -e 4000
> 
> When I saw the resulting file greatly lessened in size, that's when I tried as a test
> 
> trjconv -f traj.trr -o traj_1.trr
> 
> I knew that it was not supposed to do anything, hence my surprise upon seeing the file size decrease by ~25%.
> 
> No other flags were used.
> 
> I'll do your suggestion in 2 days. Am out of the lab till then.
> 
> Thanks
> 
> Gil Claudio
> 
> On Oct 15, 2012, at 7:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> > 
> > 
> > On 10/15/12 7:50 AM, Gil Claudio wrote:
> >> Hi Peter,
> >> 
> >> Same machine, all single precision.
> >> 
> > 
> > Run gmxcheck -f -f2 on the two trajectories to see what's going on.  Can you explain what you were trying to do?  I see no point in the trjconv command you ran.  Were there other flags that you haven't shown?  Other commands that produced strange results that led you to simplify the trjconv command down to something that (in theory) doesn't do anything?
> > 
> > -Justin
> > 
> >> On Oct 15, 2012, at 5:39 PM, "Peter C. Lai" <pcl at uab.edu> wrote:
> >> 
> >>> Was traj.trr output by the same machine/mdrun as the machine you are running
> >>> trjconv on?
> >>> 
> >>> Is traj.trr (or the mdrun that wrote it) double precision and trjconv is
> >>> compiled float (single precision)?
> >>> 
> >>> On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote:
> >>>> Hi all,
> >>>> 
> >>>> When I do the following command
> >>>> 
> >>>> trjconv -f traj.trr -o traj_1.trr
> >>>> 
> >>>> the file size of traj_1.trr is around 25% smaller than traj.trr.
> >>>> 
> >>>> Does traj_1.trr contain less data than traj.trr?
> >>>> 
> >>>> Thanks
> >>>> 
> >>>> Gil
> >>>> --
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> >>> 
> >>> --
> >>> ==================================================================
> >>> Peter C. Lai            | University of Alabama-Birmingham
> >>> Programmer/Analyst        | KAUL 752A
> >>> Genetics, Div. of Research    | 705 South 20th Street
> >>> pcl at uab.edu            | Birmingham AL 35294-4461
> >>> (205) 690-0808            |
> >>> ==================================================================
> >>> 
> > 
> > -- 
> > ========================================
> > 
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > 
> > ========================================
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