[gmx-users] Regarding g_cluster output.

[Justin Lemkul]

On 1/15/15 8:56 AM, Abhi Acharya wrote:
> Hello Gromacs users.
>
> I ran g_clustsize on a trajectory file. The output gives the cluster
> members in the last column. I don't understand, how these members are
> numbered. My trajectory contains 25001 frames whereas the members are
> numbered till 50000. The output I get is as follows:
>
> Using gromos method for clustering
> Using RMSD cutoff 0.1 nm
> The RMSD ranges from 0.0398338 to 1.58 nm
> Average RMSD is 0.10737
> Number of structures for matrix 25001
> Energy of the matrix is 6578.78 nm
>
> Found 2519 clusters
>
> Writing average structure for each cluster to clusters.pdb
> Writing all structures for the first 20 clusters with more than 1
> structures to clusters.pdb%04d.pdb
> Counted 7269 transitions in total, max 19 between two specific clusters
>
> cl. | #st  rmsd | middle rmsd | cluster members
>    1 | 575  0.106 |  44164 .087 |  39816  39988  40246  41958  41960  41968
>   42266
>      |           |             |  42290  42292  42294  42340  42342  42346
>   42352
>      |           |             |  42358  42360  42362  42364  42366  42410
>   42412
>      |           |             |  42414  42416  42418  42420  42422  42424
>   42426
>      |           |             |  42432  42434  42436  42438  42440  42442
>   42444
>      |           |             |  42452  42454  42456  42458  42460  42462
>   42478
>      |           |             |  42490  42492  42494  42534  42542  42560
>   42572
>      |           |             |  42620  42730  42878  42880  42900  42902
>   42908
>      |           |             |  42912  42914  42964  42966  42968  42970
>   42972
>      |           |             |  42974  42976  42978  42980  42982  42984
>   42990
>

The output is in time, not frame number.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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