Dear amber community,
Within the context of my work, i was testing out different clustering
algorithms implemented in the Amber18 package. When testing the Density
Peaks (DPEAKS) algorithm (Laio and Rodriguez, 2014), i received a warning:
"Warning: The dpeaks algorithm is still under development. USE WITH
CAUTION!" My question is the following: Does Amber20 include an optimized
version of this algorithm?
Additionally, if i try to run the clustering algorithm while employing the
gauss keyword, CPPTRAJ fails with segfault. Does anyone know why this
happens?
Below is a copy-paste of the segfault:
"
PARAMETER FILES (1 total):
0: ligand.prmtop, 14 atoms, 1 res, box: None, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'vac.nc' is a NetCDF AMBER trajectory with coordinates, time, Parm
ligand.prmtop (reading 2000 of 2000)
Coordinate processing will occur on 2000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'ligand.prmtop' (3 actions):
0: [autoimage]
Warning: Topology ligand.prmtop does not contain box information.
Warning: Setup incomplete for [autoimage]: Skipping
1: [rms mass first]
Target mask: [*](14)
Reference mask: [*](14)
2: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store times.
Estimated memory usage (2000 frames): 336.024 kB
----- vac.nc (1-2000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 2000 frames and processed 2000 frames.
TIME: Avg. throughput= 573065.9026 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster cluster dpeaks epsilon 0.2 dvdfile disvsdens.dat choosepoints
manual distancecut 0.2 densitycut 0.2 runavg runningave.dat deltafile
dis-minus-runavg.dat gauss rms mass sieve 10 random out cnumbervtime.dat
sil Sil summary summary.dat info info.dat cpopvtime cpopvtime.agr normframe
repout rep repfmt pdb singlerepout represents.nc singlerepfmt netcdf avgout
AvgFrame_Cluster avgfmt restart]
Starting clustering.
Mask [*] corresponds to 14 atoms.
Random_Number: seed is <= 0, using wallclock time as seed (6365)
Estimated pair-wise matrix memory usage: > 79.664 kB
Pair-wise matrix set up with sieve, 2000 frames, 200 sieved frames.
Calculating pair-wise distances.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
Memory used by pair-wise matrix and other cluster data: 88.512 kB
Starting DPeaks clustering. Using Gaussian kernel to calculate density.
idx= 398, bandwidth= 0.147002
Max dist= 1.16382
Point 7 (frame 208, density 7.31656) selected as candidate for cluster 0
Point 14 (frame 942, density 6.61173) selected as candidate for cluster 1
Point 29 (frame 664, density 5.97075) selected as candidate for cluster 2
Point 60 (frame 1274, density 4.57396) selected as candidate for cluster 3
Point 68 (frame 113, density 4.40185) selected as candidate for cluster 4
Point 77 (frame 1737, density 4.09013) selected as candidate for cluster 5
Point 90 (frame 1566, density 3.33413) selected as candidate for cluster 6
Point 120 (frame 192, density 2.20433) selected as candidate for cluster 7
Point 121 (frame 1278, density 2.17273) selected as candidate for cluster 8
Point 124 (frame 1347, density 2.12788) selected as candidate for cluster 9
Point 136 (frame 622, density 1.71068) selected as candidate for cluster 10
Point 149 (frame 643, density 1.42446) selected as candidate for cluster 11
Point 150 (frame 719, density 1.42032) selected as candidate for cluster 12
Point 151 (frame 572, density 1.36985) selected as candidate for cluster 13
Point 158 (frame 1404, density 1.10734) selected as candidate for cluster 14
Point 160 (frame 495, density 1.0566) selected as candidate for cluster 15
Point 164 (frame 1157, density 0.981053) selected as candidate for cluster
16
Point 165 (frame 1675, density 0.980377) selected as candidate for cluster
17
Point 169 (frame 371, density 0.924646) selected as candidate for cluster 18
Point 170 (frame 984, density 0.908064) selected as candidate for cluster 19
Point 171 (frame 1065, density 0.898682) selected as candidate for cluster
20
Point 173 (frame 1757, density 0.877534) selected as candidate for cluster
21
Point 175 (frame 1544, density 0.840694) selected as candidate for cluster
22
Point 178 (frame 245, density 0.806564) selected as candidate for cluster 23
Point 180 (frame 481, density 0.781851) selected as candidate for cluster 24
Point 183 (frame 1038, density 0.630666) selected as candidate for cluster
25
Point 186 (frame 504, density 0.590398) selected as candidate for cluster 26
Point 187 (frame 1874, density 0.577614) selected as candidate for cluster
27
Point 192 (frame 644, density 0.399897) selected as candidate for cluster 28
Point 195 (frame 1463, density 0.343491) selected as candidate for cluster
29
Identified 30 cluster centers from density vs distance peaks.
Killed
"
Here is the input file i supplied:
"
parm ligand.prmtop
trajin vac.nc
autoimage
rms mass first
cluster cluster dpeaks epsilon 0.2 dvdfile disvsdens.dat choosepoints
manual distancecut 0.2 densitycut 0.2 runavg runningave.dat deltafile
dis-minus-runavg.dat gauss \
rms mass \
sieve 10 random \
out cnumbervtime.dat \
sil Sil \
summary summary.dat \
info info.dat \
cpopvtime cpopvtime.agr normframe \
repout rep repfmt pdb \
singlerepout represents.nc singlerepfmt netcdf \
avgout AvgFrame_Cluster avgfmt restart
run
go
quit
"
Thank you in advance,
Gilberto Pereira
PhD student at the LABORATOIRE D’INGÉNIERIE DES FONCTIONS MOLÉCULAIRES,
Univeristy of Strasbourg, France.
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Received on Thu Jul 02 2020 - 09:00:03 PDT
