[gmx-users] compressed tng file

[Ahmet Yıldırım]

Hi,

It would be good if GROMACS had ability to write compressed velocities and coordinates from mdrun with -o flag. 

By the way I did a small test:
The trjconv with -vel flag compressed a trr file of 14 GB  to tng file of 2.6 GB. It means about a factor of five. 



Ahmet Yıldırım


25 Eki 2015 tarihinde 04:18 saatinde, Mark Abraham <mark.j.abraham at gmail.com> şunları yazdı:

> 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.
>>>>> 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
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