[gmx-users] compressed tng file

[Mark Abraham]

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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
>
>
> --
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.