Thank you, Carlos, that's even better!
Karolina
2016-02-11 12:15 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> We frequently read in 2 trajectories then do cluster analysis, and compare
> the population of each cluster in trajectory 1 vs 2.this gives you error
> bars on the population of each cluster. It's similar to 2drmsd but gives
> you something more quantitative.
> On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote:
>
> > 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 Thu Feb 11 2016 - 03:30:05 PST
