Autoimaging prior to clustering is only necessary if your distance
metric will involve more than 1 molecule, e.g. the conformation of a
protein dimer. Otherwise it doesn't matter.
-Dan
On Sat, Jan 7, 2017 at 5:33 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir
>
> before i perform cluster on my trajectory i had done autoimage.
> since i had included the option for cluster trajectories, trajectory
> corresponding to each cluster was also formed.
> I tried to cluster the most populated cluster again. i want to know
> whether the cluster trajectories formed in the first step is
> autoimaged? or should i autoimage that again before i do my second
> cluster?
>
>
>
>
> On 1/5/17, Mary Varughese <maryvj1985.gmail.com> wrote:
>> Thank you very much.
>>
>> It was very much helpful especially that script in supp material.
>>
>> Thank you
>>
>> On Thu, Jan 5, 2017 at 7:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> See also the clustering script in part 7 of the supporting info here:
>>> http://pubs.acs.org/doi/abs/10.1021/jp4125099
>>>
>>> -Dan
>>>
>>> On Thu, Jan 5, 2017 at 7:48 AM, Christina Bergonzo <cbergonzo.gmail.com>
>>> wrote:
>>> > Hi,
>>> >
>>> > You can take a look at the supporting information of this paper:
>>> > Highly sampled tetranucleotide and tetraloop motifs enable evaluation
>>> > of
>>> > common RNA force fields
>>> > <https://scholar.google.com/citations?view_op=view_citation&hl=en&user=
>>> d4JoelsAAAAJ&citation_for_view=d4JoelsAAAAJ:In6cVmBjs0IC>
>>> > C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
>>> > RNA 21 (9), 1578-1590
>>> >
>>> > http://rnajournal.cshlp.org/content/suppl/2015/06/19/rna.
>>> 051102.115.DC1/SuppMaterial.pdf
>>> >
>>> > There is a CPPTRAJ command which performs combined clustering on 8
>>> > trajectories.
>>> >
>>> > Hope this helps,
>>> > Christina
>>> >
>>> > On Thu, Jan 5, 2017 at 5:59 AM, Mary Varughese <maryvj1985.gmail.com>
>>> wrote:
>>> >
>>> >> Sir
>>> >>
>>> >>
>>> >> in combined clustering, could i compare more than two trajectories? If
>>> >> so is there any difference in the command option
>>> >> split ..Frameno...
>>> >>
>>> >> Also in split_summary.dat is there any useful information.
>>> >>
>>> >> how could i infer the convergence of the trajectory DBI , pSF
>>> >>
>>> >> Please give me some idea
>>> >>
>>> >>
>>> >> Thanking you
>>> >>
>>> >>
>>> >> mary varughese
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > ------------------------------------------------------------
>>> ---------------------------
>>> > Christina Bergonzo
>>> > Postdoctoral Researcher
>>> > Department of Medicinal Chemistry, University of Utah
>>> > http://home.chpc.utah.edu/~cheatham/
>>> > ------------------------------------------------------------
>>> ---------------------------
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sun Jan 08 2017 - 11:00:02 PST
