[gmx-users] Accelerating data analysis.

[Mark Abraham]

Hi,

Yes. There is no intelligence about .trr reading (unlike .xtc) so it reads
every frame until one that satisfies your constraint. You will have a
better time implementing Erik's strategy if you break the trajectory into
parts with trjconv, convert it to .xtc, or write it as .xtc in the first
place. See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Tue, Sep 15, 2015 at 2:59 PM Dawid das <addiw7 at googlemail.com> wrote:

> Something is wrong here. I use following command:
>
> g_rms -tu us -b 0.9 -e 1.0 -s npt-md2.tpr -f npt-md2.trr -n index.ndx -o
> rmsd-protein.xvg
>
> and g_rmsd still starts from 0 and it says "Skipping frame..." and it seems
> it will skip all frames (as it would read it) until 0.9 us.
> Is that what I should expect?
>
>
> 2015-09-15 13:45 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>
> > Dear All,
> >
> > Thank you all. Especially for your tip Erik ;).
> >
> > Dawid
> >
> > 2015-09-15 13:42 GMT+01:00 Erik Marklund <erik.marklund at chem.ox.ac.uk>:
> >
> >> Dear Dawid,
> >>
> >> The best thing I can think of is to analyse different parts of the
> >> trajectory in parallel, using separate g_rms processes, then
> concatenating
> >> the output. Use -b and -e options to limit the analysis to specific
> >> intervals.
> >>
> >> Kind regards,
> >> Erik
> >>
> >> > On 15 Sep 2015, at 13:37, Dawid das <addiw7 at googlemail.com> wrote:
> >> >
> >> > Dear Gromacs Experts,
> >> >
> >> > I have an enormous *trr file, which has 1 000 000 points. Now, I know
> >> that
> >> > I can modify this file with trjconv, but let's say I do not want to do
> >> it,
> >> > but I want to have my 1 000 000 points in *xvg file when I use g_rms
> for
> >> > instance.
> >> > Is there a way to accelarate it?
> >> >
> >> > Best wishes,
> >> >
> >> > Dawid Grabarek
> >> > --
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