Nice! I had no idea of *crdaction* :)
This is more what I was looking for because I only have to load the
trajectory once.
On Thu, Jul 6, 2017 at 4:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> In addition to the start/stop/offset args to trajin that Hai
> mentioned, this can also be done via coordinate data sets:
>
> parm myparm.parm7
> loadcrd mytraj.nc name Crd0
> crdaction Crd0 rms <rms args> crdframes <start0>,<stop0>,<offset0>
> crdaction Crd0 rms <rms args> crdframes <start1>,<stop1>,<offset1>
> crdaction Crd0 rms <rms args> crdframes <start2>,<stop2>,<offset2>
>
> If memory is an issue use 'loadtraj' to keep the coords on disk
> (potential issue there is that TRAJ coords data sets do not get
> modified).
>
> -Dan
>
> On Thu, Jul 6, 2017 at 2:41 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > Dear Amber users,
> >
> > I want to do RMS on different trajectory fragments. Right now I extract
> one
> > fragment and save to file, then read the file as my new trajectory to
> > calculate RMS. This for each fragment :(
> >
> > Is there a way to avoid this writing/reading? The RMS command does not
> seem
> > to have *start* and *stop* options, like *atomicfluct *does.
> >
> > Best,
> > .Jose
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 06 2017 - 13:30:03 PDT
