[gmx-users] Accelerating data analysis.

[Dawid das]

Thank you again. So after all I still need trjconv.


2015-09-15 14:24 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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