[gmx-users] compressed tng file

[Mark Abraham]

Hi,

I suspect there's no ability to actually write compressed velocities from
mdrun, unless -o .tng defaults to gzip for velocities within libtng (and
that won't give a factor of three). I suspect it could be added readily,
but it's a question of what needs exist and how to express them in new mdp
options that map to what TNG can do.

Ahmet, what capability would best suit your need?

Mark

On Sat, 24 Oct 2015 21:56 David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On 24/10/15 21:53, Ahmet Yıldırım wrote:
> > 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.
> Mark says you need to use -x
> Just try it.
> And there may be compressed-v options to, check your mdout.mdp
>
> >
> > 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.
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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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