[gmx-users] compressed tng file

[Ahmet Yıldırım]

nstxout-compressed       = 20
compressed-x-precision   = 1000
compressed-x-grps        = System

Those mdp options will compress only coordinates in the tng file with -x
flag. But I want to compress both coordinates and velocities in the tng
file with -o option. It seems that GROMACS 5.1 doesn't do it.
I think the best way is to convert the trr file to the tng file using
trjconv -vel.

2015-10-24 22:30 GMT+03:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> On Sat, Oct 24, 2015 at 9:17 PM David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
> > On 24/10/15 21:10, Mark Abraham wrote:
> > > Hi,
> > >
> > > I forget the details, but why are you supposing a factor of three? The
> > best
> > > you can do with storing full-precision trajectory information to -o
> .tng
> > is
> > > gzip compression, which is well known not to be great for MD
> > trajectories.
> > > -x .tng is another matter.
> > >
> > You have to play with the mdp options, something like
> > ; Output frequency and precision for xtc file =
> > nstxout-compressed       = 20
> > compressed-x-precision   = 1000
> > ; This selects the subset of atoms for the xtc file. You can =
> > ; select multiple groups. By default all atoms will be written. =
> > compressed-x-grps        = System
> >
> > and probably similar for velocities.
> > @Mark: the factor of three comes from typical xtc compression of
> > coordinates.
> >
>
> Right. But getting the format still needs mdrun -x *.tng, not -o. We
> haven't written the code to put all kinds of trajectory output into the one
> .tng file.
>
> Mark
>
>
> > > Mark
> > >
> > > On Sat, Oct 24, 2015 at 8:24 PM Ahmet Yıldırım <ahmedo047 at gmail.com>
> > wrote:
> > >
> > >> Dear users,
> > >>
> > >> In order to get the tng file smaller than trr file I am using the
> > following
> > >> command but I get the same file size as trr file. Whereas the tng file
> > file
> > >> should be about 3 times smaller than the trr file.
> > >>
> > >> I wonder if anybody has any clue what's wrong?
> > >>
> > >> gmx_d mdrun -v -s md.tpr -cpo md.cpt -o md.tng -c md.gro -e md.edr -g
> > >> md.log
> > >>
> > >>
> > >> --
> > >> Ahmet Yıldırım
> > >> --
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> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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Ahmet Yıldırım