[gmx-users] compressed tng file

[David van der Spoel]

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.

> 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