Dear Mark,
it's so simple and so brilliant!
Thank you very much.
Have a nice weekend.
Karolina
2016-02-12 10:20 GMT+01:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> Hi Karolina,
>
> The 2D-RMSD plot would be OK, but we're interested in comparing the
> > movement of each amino acid. The question we want to answer is - does
> this
> > amino acid behave _like this_ in both simulations or just in one case?
> >
> > To answer this question, you can just to a standard RMSF (by residue) for
> each trajectory, and then plot them in one plot.
>
> --Marc
>
>
>
> > 2016-02-11 16:40 GMT+01:00 Osman, Roman <roman.osman.mssm.edu>:
> >
> > > Karolyn's
> > > My colleague Mihaly Mezei implemented a 2D rmsd comparison of two
> > > trajectories.
> > > Please contact him. Mihaly.mezei.mssm.edu
> > >
> > > I used it and it's a great tool
> > >
> > > Roman Osman
> > > Sent from my iPhone
> > >
> > > > On Feb 11, 2016, at 4:45 AM, Karolina Markowska <
> > markowska.kar.gmail.com>
> > > wrote:
> > > >
> > > > Thank you, Bill and Anselm for your advices,
> > > >
> > > > I think I will try the 2D-RMSD-plot first.
> > > >
> > > > Have a nice day!
> > > > Karolina
> > > >
> > > > 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
> > > >
> > > >> Dear Karolina,
> > > >>
> > > >> AFAIK a 'reference' is limited to a single structure.
> > > >>
> > > >> Reading in two trajectories in a row should be no problem for
> cpptraj,
> > > >> as you can give several trajin commands.
> > > >> For the comparison of the two trajectories you could then use e.g. a
> > > >> 2D-RMSD-plot or perform a cluster analysis on the combined
> > trajectories
> > > >> with a subsequent inspection of the distribution of the cluster
> > > >> structures between the trajectories. Or you could monitor some other
> > > >> properties of interest and compare those values.
> > > >>
> > > >> Regards,
> > > >>
> > > >> Anselm
> > > >>
> > > >>
> > > >> Am 11.02.2016 10:07, schrieb Karolina Markowska:
> > > >>> Dear Amber Users,
> > > >>>
> > > >>> I have two simulations with the same system and I would like to
> > compare
> > > >>> them. Mostly I would like to check if I'm having the same protein
> > > >>> conformations in these two simulations. Does Amber software
> provide a
> > > >> tool
> > > >>> for that kind of analysis?
> > > >>>
> > > >>> I wanted to use cpptraj and use the first trajectory as reference,
> > add
> > > >> the
> > > >>> second one by trajin and calculate rmsd between them, but cpptraj
> > uses
> > > >> only
> > > >>> the first frame from that file. Can I make cpptraj to read whole
> > > >> trajectory
> > > >>> as a reference?
> > > >>> The script looked like that:
> > > >>>
> > > >>> parm protein.prmtop
> > > >>> reference sim1.nc
> > > >>> trajin sim2.nc
> > > >>> autoimage
> > > >>> strip :WAT
> > > >>> strip :Na+
> > > >>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
> > > >>> quit
> > > >>>
> > > >>> | sim1.nc is the trajectory of the first simulation and sim2.nc is
> > the
> > > >>> trajectory from the second simulation.
> > > >>>
> > > >>> Thanks for your help.
> > > >>> Best regards,
> > > >>> Karolina Markowska
> > > >>> PhD student
> > > >>> _______________________________________________
> > > >>> AMBER mailing list
> > > >>> AMBER.ambermd.org
> > > >>>
> > >
> >
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Received on Fri Feb 12 2016 - 03:00:03 PST
