[gmx-users] compressed tng file

[David van der Spoel]

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.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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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