Yes. Thanks.
On Aug 29, 2014 12:21 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Yes (I assume you're talking about the single representative traj).
>
> On Fri, Aug 29, 2014 at 10:01 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > Quick followup question. if you output the representative frames, it
> writes
> > them in the order of clustering, correct? eg. 0, 1, 2, etc.
> >
> >
> > On Fri, Aug 29, 2014 at 11:40 AM, Jonathan Gough <
> jonathan.d.gough.gmail.com
> >> wrote:
> >
> >> As always, very helpful. Thanks Dan!
> >> On Aug 29, 2014 11:23 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> >>
> >>> Hi,
> >>>
> >>> On Fri, Aug 29, 2014 at 8:56 AM, Jonathan Gough
> >>> <jonathan.d.gough.gmail.com> wrote:
> >>> > When running a cluster command, the output lists a "representative
> >>> frames"
> >>> > for each cluster. I am guessing that I could use that number and the
> >>> > origional trajectories to generate a .rst file and therefore a .pdb.
> >>> > If so, how does one (what is the best way to) do that (especially
> if
> >>> I
> >>> > have more than one trajectory as the input)?
> >>>
> >>> Representative frame numbering is relative to the total number of
> >>> frames read in. So if you have e.g. two trajectories of 100 frames
> >>> each that you clustered on, and your representative frames are 90,
> >>> 120, and 150, you can get them by using 'trajout' with the
> >>> 'onlyframes' keyword, e.g.
> >>>
> >>> trajin traj1.nc
> >>> trajin traj2.nc
> >>> trajout rep.rst7 restart onlyframes 90,120,150
> >>>
> >>> > In looking through the manual (section 28.13.1) I now see two
> commands
> >>> that
> >>> > might have performed the task for me when I ran the calculation
> >>> > (singlereoout and repout)
> >>> > Can someone provide some insight on their use and the difference
> >>> between
> >>> > the two?
> >>>
> >>> I think the manual is fairly clear here:
> >>>
> >>> "repout <repprefix>: Write representative frames to separate files
> >>> named <repprefix>.X.<ext>, where X is the cluster number and <ext> is
> >>> a format-specific filename extension.
> >>> singlerepout <trajfilename> Write all representative frames to single
> >>> trajectory named <trajfilename>."
> >>>
> >>> So the only difference is that 'singlerepout' puts all of the
> >>> representatives in a single file, while 'repout' puts them in separate
> >>> files.
> >>>
> >>> > Also, can these commands be used after a clustering calculation
> has
> >>> been
> >>> > performed (eg. saving the processing time of re-running the
> clustering
> >>> > algorithm?
> >>>
> >>> Not yet, although that support is planned. Your best bet is to use
> >>> 'trajout onlyframes' as mentioned above. However, note that you can
> >>> save some time when re-running the same clustering calculation
> >>> multiple times by saving and reusing the pair-wise distance matrix via
> >>> the 'savepairdist' and 'loadpairdist' keywords. For most purposes it's
> >>> enough to just add the 'loadpairdist' keyword; this will trigger
> >>> saving the pairwise distance matrix file on the first run and re-read
> >>> it on subsequent runs. Be careful when using this though because if
> >>> you change your distance metric (by e.g. changing your rms mask) the
> >>> matrix will no longer be valid. Cpptraj can detect when the number of
> >>> frames in the matrix changes and recalculate, but currently has no way
> >>> to determine if more subtle things in the matrix change.
> >>>
> >>> Hope this helps,
> >>>
> >>> -Dan
> >>>
> >>> >
> >>> >
> >>> > If it's helpful - here are the cpptraj commands I used to generate my
> >>> > clustering results.
> >>> >
> >>> > parm nowat.dimer.prmtop
> >>> > trajin prod01-24-dimer.nc
> >>> > trajin prod25-30-dimer.nc
> >>> > cluster C1 :1-164 clusters 10 sieve 10 epsilon 4.0 out cnumvtime.dat
> >>> > summary avg.summary.dat clusterout cl clusterfmt netcrd
> >>> > run
> >>> > quit
> >>> > _______________________________________________
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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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> >>>
> >>
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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 Fri Aug 29 2014 - 09:30:03 PDT
