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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Received on Fri Feb 26 2016 - 21:30:05 PST
