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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--
-------------------------
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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Received on Thu Jul 06 2017 - 13:30:02 PDT
