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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Received on Fri Aug 29 2014 - 09:30:02 PDT
