Hi Anselm,
Thank you for the suggestion. I realized I should not load traj2.nc in
cpptraj.
On Tue, Jul 18, 2023 at 10:11 PM Dr. Anselm Horn via AMBER <
amber.ambermd.org> wrote:
> Yun,
>
> the description of rms2d in the manual (AmberTools23 p. 830) would
> suggest something like:
>
> parm xyz.prmtop
> trajin traj1.nc
> rms2d .CA out test2drms.gnu reftraj traj2.nc
>
> Does this work?
>
> Best,
>
> Anselm
>
> PD Dr.rer.nat.
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
> Am 18.07.2023 um 08:06 schrieb yunshi11 via AMBER:
> > Hi all,
> >
> > I am trying to compare traj1.nc vs traj2.nc. They have the same
> topology in
> > xyz.prmtop.
> >
> > Using rms2d, how to generate a 2d rms comparison?
> >
> > I tried the following in cpptraj but it gave me a comparison of traj1.nc
> vs
> > traj1.nc instead:
> >
> > parm xyz.prmtop
> > loadcrd traj2.nc
> > trajin traj1.nc
> > rms2d .CA out test2drms.gnu reftraj traj1.nc
> >
> > Thanks,
> > Yun
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Mon Jul 24 2023 - 23:00:03 PDT
