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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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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
