any insight?
Can ptraj write trajectories as netcdf? what is the most compact way of
writing trajectories as the output of a clustering in ptraj
when I tried using 'netcdf' or 'cdf' for all, I got "WARNING: invalid file
format netcdf/cdf!"
am I missing something?
On Sun, Jan 4, 2015 at 1:05 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> Dan,
>
> You mentioned that I could ask for help with clustering using ptraj... so
> I'm going to ask for a little bit of help/guidance/insight.
>
> I read through the manual, your paper, compiled ptraj, and successfully
> run some test clustering.
>
> My questions stem from the application of your paper and the
> implementation of it in ptraj. Specifically, I want to make sure I'm not
> being overly redundant. (I fully understand that this is more of an Art
> form that a prescriptive procedure)
>
> Not knowing what the cluster count is, it seems that the best way to
> proceed is to:
> 1. run CobWeb (clusters -1) to get an idea of the number (range of
> numbers) for natural clusters in a given data set (where the atom masks are
> the same)
> 2. Then run averagelinkage, means, and/or SOM algorithms with cluster
> values around that implicated by CobWeb and use the pSF and DBI to assess
> efficacy and choose a specific cluster count. Then proceed with analysis...
>
> I did notice that in the implementation of the agglomerative algorithms
> the ClusterMerging.txt
> file gives pSF and DBI values for different numbers of clusters. It was
> noted that one can set clusters to 1 and then use ReadMerge to generate
> other numbers of clusters. I'm not sure exactly how to use this type of
> functionality, but I was wondering, can you just run cluster 1, then use
> the results generated in ClusterMerging.txt to decide on the number of
> clusters and critical distance (as per your paper - low DBI and high pSF)
> for an agglomerative algorithm?
>
> If I am looking to test out and compare different clustering algorithms,
> is there a way to tell ptraj to NOT print out the full clusters? (if all I
> am trying to do is assess the representative structures and the clustering
> metrics)
>
> Any insight would be appreciated.
>
> Thanks,
> Jonathan
>
>
>
> On Mon, Dec 22, 2014 at 9:59 PM, Jonathan Gough <
> jonathan.d.gough.gmail.com> wrote:
>
>> As Always, Very Helpful. Thanks Dan!
>>
>> On Mon, Dec 22, 2014 at 9:30 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> The ptraj code is still there in Amber 14, it's just not built by
>>> default.
>>> You need to go to the AmberTools/src/ptraj subdirectory and type 'make
>>> install' (after configuring serial of course). Let me know if you hit any
>>> roadblocks.
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> On Monday, December 22, 2014, Jonathan Gough <jonathan.d.gough.gmail.com
>>> >
>>> wrote:
>>>
>>> > That makes sense.
>>> >
>>> > Have all the algorithms from your "J. Chem. Theory Comput., Vol. 3,
>>> No. 6,
>>> > 2007" paper been ported over to cpptraj?
>>> >
>>> > I just realized that ptraj is not in Amber14, do you have a
>>> recommendation
>>> > on how best to install/compile ptraj (AmberTools13) alongside of a
>>> > pre-existing Amber14 installation?
>>> >
>>> > Thanks,
>>> > Jonathan
>>> >
>>> > On Fri, Dec 19, 2014 at 11:52 AM, Daniel Roe <daniel.r.roe.gmail.com
>>> > <javascript:;>> wrote:
>>> >
>>> > > Hi,
>>> > >
>>> > > The pseudo-F calculation is not yet in the released version of
>>> > > cpptraj, but it has been in the development version for some time. It
>>> > > might possibly be released as part of an update. You could *maybe*
>>> > > calculate it manually but it would take quite a bit of scripting. You
>>> > > would need to manually calculate the centroid for each cluster and a
>>> > > centroid for all clusters (doing rms-fitting as necessary if that is
>>> > > your distance metric), then calculate the between-group and
>>> > > within-group sum of squares for each cluster. If for some reason you
>>> > > really need the pseudo-F statistic right away you'll have to use
>>> > > clustering in ptraj for now.
>>> > >
>>> > > -Dan
>>> > >
>>> > > On Thu, Dec 18, 2014 at 3:54 PM, Jonathan Gough
>>> > > <jonathan.d.gough.gmail.com <javascript:;>> wrote:
>>> > > > Dear All,
>>> > > >
>>> > > > Is there a way to compute the pseudo F-statistic
>>> > > > (pSF), as per J. Chem. Theory Comput., Vol. 3, No. 6, 2007,
>>> > > > when clustering in cpptraj?
>>> > > >
>>> > > > Thanks
>>> > > > Jonathan
>>> > > > _______________________________________________
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>>> > > > AMBER.ambermd.org <javascript:;>
>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > -------------------------
>>> > > 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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>>> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> > _______________________________________________
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>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>> --
>>> -------------------------
>>> 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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Received on Thu Jan 08 2015 - 08:30:04 PST
