Just to add a bit to what Carlos said, CPPTRAJ does this kind of
combined cluster analysis natively. You just read in your two separate
trajectories, and cluster on them with the 'summarysplit' and
'splitframe' keywords. For example, if you have two trajectories each
with 1000 frames you could cluster like so:
parm myparm.parm7
trajin traj1.nc
trajin traj2.nc
cluster <clustering options> summarysplit split.dat splitframe 1000
This can be used to compare any number of trajectories.
Another method that we have been using to compare different
trajectories is to calculate the Kullback-Leibler divergence to
quantify the overlap of various distributions calculated from each
trajectory - in particular the principal component projection
histograms. For some examples of these kinds of calculations (as well
as example cpptraj scripts) see these articles and their supporting
info:
http://pubs.acs.org/doi/abs/10.1021/jp4125099
http://pubs.acs.org/doi/abs/10.1021/ct400862k
Hope this helps,
-Dan
On Thu, Feb 11, 2016 at 4:27 AM, Karolina Markowska
<markowska.kar.gmail.com> wrote:
> 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
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> >
>> >
>> > _______________________________________________
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>> >
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 11 2016 - 07:30:04 PST
