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
> > >>> _______________________________________________
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> > >>>
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Received on Fri Feb 12 2016 - 01:30:05 PST
