HI,
It is little confusing what you are trying to do.
Instead, I will suggest you what I usually do.
Step 1- After I finish my simulations (usually n=3), using cpptraj I strip all waters and ions (you may keep them), autoimage the trajectories and save autoimaged trajectory (without water and ions in my case). Repeat this for each independent runs.
Step2- While performing combined clustering, now load all autoimaged trajectories and perform clustering.
Hope this helps
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Mary Varughese [mailto:maryvj1985.gmail.com]
Sent: Saturday, January 07, 2017 4:03 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj clustering doubt
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&u
>> > ser=
>> 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
>>
>
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Received on Sat Jan 07 2017 - 07:00:02 PST
