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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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