Good tip on loading the clustering trajectory separately - I will try that. Thanks!
And I’m using CPPTRAJ V16.00 …
Yinglong
> On Jun 1, 2016, at 7:38 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Remember, by default COORDS data sets are saved in memory so that will
> reduce the total memory available as well. You can load the
> coordinates as a TRAJ data set instead so that the data stays on the
> disk. The only issue there is that TRAJ data sets cannot be modified,
> so you will have to save the trajectory separately. So just have input
> for the first run go something like:
>
> parm protein.prmtop
> trajin md-reimaged.nc
> ## RMSD
> reference pro.pdb
> rms reference out rmsd-clustering.dat
> :5-27,42-62,80-101,122-144,167-189,210-230,245-264.CA
> rmsd :278.*&!.H= reference nofit out rmsd-lig-clustering.dat
> strip :1-277 outprefix strip
> trajout forcluster.nc
>
> Then input for the second run would be something like this:
>
> parm strip.protein.prmtop
> loadtraj forcluster.nc name MyTraj
> cluster crdset MyTraj ...
>
> Now the only large memory requirement will be for the pairwise matrix.
> In the meantime I'm working on some code that will eliminate the
> pairwise matrix memory requirement (at the cost of being slower). Hope
> to get that done soon.
>
> -Dan
>
>
> On Tue, May 31, 2016 at 5:14 PM, Yinglong Miao <yimiao.ucsd.edu> wrote:
>> Just a little more information: I previously ran cpptraj within a batch
>> script, now as I run it alone, it output the following error:
>>
>> 0% 10% 20% 30% Segmentation fault (core dumped)
>>
>> Thanks,
>> Yinglong
>>
>> On Tue, May 31, 2016 at 12:44 PM, Yinglong Miao <yimiao.ucsd.edu> wrote:
>>
>>> Hi Dan,
>>>
>>> Thanks for your reply. I also tried DBSCAN and seems dpeaks works better -
>>> really hope dpeaks with full functionality will be available soon.
>>>
>>> And here is my input file:
>>>
>>> ----
>>> parm protein.prmtop
>>> trajin md-reimaged.nc
>>> ## RMSD
>>> reference pro.pdb
>>> rms reference out rmsd-clustering.dat
>>> :5-27,42-62,80-101,122-144,167-189,210-230,245-264.CA
>>> rmsd :278.*&!.H= reference nofit out rmsd-lig-clustering.dat
>>> strip :1-277
>>> cluster C0 \
>>> dpeaks epsilon 1 dvdfile density_vs_dist.dat choosepoints auto
>>> distancecut 1.0 runavg runavg.dat deltafile delta.dat \
>>> rms :1@*&!.H= nofit \
>>> sieve 1 \
>>> out cnumvtime.dat \
>>> summary summary.dat \
>>> info info.dat \
>>> cpopvtime cpopvtime.agr normframe \
>>> repout rep repfmt pdb \
>>> singlerepout singlerep.nc singlerepfmt netcdf \
>>> avgout Avg avgfmt restart
>>> go
>>> ----
>>>
>>> Yinglong
>>>
>>>
>>> On Tue, May 31, 2016 at 12:03 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> On Tue, May 31, 2016 at 11:36 AM, Yinglong Miao <yinglong.miao.gmail.com>
>>>> wrote:
>>>>> This may be also a question on the Users mailing list, but as I try the
>>>>> cpptraj density peaks (dpeaks) clustering (which is great!), I notice
>>>> the
>>>>> following warning regarding seiving frames:
>>>>> ...
>>>>> Restoring sieved frames.
>>>>> FIXME: Adding sieved frames not yet supported.
>>>>>
>>>>> I'm wondering whether this will be coded in the near future.
>>>>
>>>> Eventually, 'dpeaks' clustering is still under development and I don't
>>>> have a time frame for when it will be complete. As is stated in the
>>>> output, 'dpeaks' as currently implemented should be used with caution.
>>>> You may want to try the DBSCAN method which also density based and is
>>>> a little better tested.
>>>>
>>>>> Also is there
>>>>> a limit on the data size for the clustering other than memory usage? The
>>>>> workstation I'm running has ~64G memory, but the program exited in the
>>>>> middle of matrix calculation (crashed?) even with apparently enough
>>>> memory:
>>>>>
>>>>> Estimated pair-wise matrix memory usage: > 16.587 GB
>>>>> Pair-wise matrix set up, 91068 frames
>>>>> 0% 10% 20% 30% mkdir: cannot create directory
>>>>> `cluster-dpeaks-e1-ncstep1-sieve1': File exists
>>>>
>>>> That doesn't look like a memory error to me. Can you provide your
>>>> exact cpptraj input?
>>>>
>>>> -Dan
>>>>
>>>>>
>>>>> Any suggestions will be appreciated,
>>>>>
>>>>> Yinglong
>>>>>
>>>>> Yinglong Miao, Ph.D.
>>>>> Research Specialist I, Howard Hughes Medical Institute
>>>>> Assistant Project Scientist, Department of Pharmacology
>>>>> University of California, San Diego
>>>>> Tel: 858-822-0255; Email: yimiao.ucsd.edu
>>>>> http://mccammon.ucsd.edu/~ymiao/
>>>>> http://gamd.ucsd.edu
>>>>> _______________________________________________
>>>>> AMBER-Developers mailing list
>>>>> AMBER-Developers.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------
>>>> 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-Developers mailing list
>>>> AMBER-Developers.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>
>>>
>>>
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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-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
---
Yinglong Miao, Ph.D.
Prof. J. Andrew McCammon Group
Research Specialist I, Howard Hughes Medical Institute
Assistant Project Scientist, Department of Pharmacology
University of California, San Diego
Tel: 858-822-0255; Email: yimiao.ucsd.edu
http://mccammon.ucsd.edu/~ymiao/
http://gamd.ucsd.edu
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Received on Wed Jun 01 2016 - 10:00:03 PDT
