Never mind, I think you meant to reply to Gerald but actually quoted me.
Hai
On Friday, February 26, 2016, Hai Nguyen <nhai.qn.gmail.com> wrote:
> You might misunderstand me (or my sentence is not clear). I was talking
> about ASCII file. I meant if using this file type, the original output file
> size is very big and waste disk space. Gzipping only happens after the
> simulation finishes.
>
> Hai
>
> On Friday, February 26, 2016, Jason Swails <jason.swails.gmail.com
> <javascript:_e(%7B%7D,'cvml','jason.swails.gmail.com');>> wrote:
>
>> On Sat, Feb 27, 2016 at 12:05 AM, Nhai <nhai.qn.gmail.com> wrote:
>>
>> >
>> > > On Feb 26, 2016, at 2:34 PM, Gerald Monard <
>> > Gerald.Monard.univ-lorraine.fr> wrote:
>> > >
>> > >
>> > >
>> > >> On 02/26/2016 10:52 PM, Adrian Roitberg wrote:
>> > >>
>> > >>
>> > >>> On 2/26/16 4:47 PM, Gerald Monard wrote:
>> > >>> Hi,
>> > >>>
>> > >>> Not against, but as a regular pymol user, I won't be able to load
>> > >>> trajectories without converting back to text format...
>> > >>>
>> > >>> Gerald, who really needs to learn VMD someday...
>> > >>
>> > >> no,no, The proper warning is Gerald, who will learn that netcdf saves
>> > >> tons of time and disk space !
>> > >
>> > > I am not that convinced by the disk space: when I gzip my text file, I
>> > > usually get smaller files that the netcdf ones.
>> >
>> > But you still need larger disk before doing the zipping :p. Zipping 100
>> GB
>> > of text file is pain to me.
>> >
>>
>> ​Well as Dan pointed out, the reason that ASCII trajectories compress
>> smaller than NetCDF ones is because they hold less information. NetCDF
>> trajectories store coordinates in full single precision (12 bytes per atom
>> per frame). ASCII trajectories store numbers in 10F8.3 format, which
>> isn't
>> even close to full single precision. Not to mention that you've trashed
>> your whole trajectory once atoms move more than 1000 A away in the
>> negative
>> x, y, or z directions.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
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Received on Fri Feb 26 2016 - 21:30:07 PST
