Dear all,
I have been trying to cluster my Gaussian Accelerated MD trajectory of a
protein-nucleic acid system using the following script.
parm noions.prmtop
trajin gamd2.nc
loadcrd gamd2.nc 1 last 5 clus_crd
cluster hieragglo epsilon 3 clusters 10 averagelinkage rms :1-1362 mass
sieve 10 out clus_out.dat summary clus_summary.dat info clus_info3.dat
repout rep3 repfmt pdb
The trajectory has 250000 frames (500ns dt =0.002 with frames saved for
every 1000 steps). The clustering proceeds for 10-20% and gets killed.
Could someone suggest any way out of this?
Thanks in advance.
Regards,
Sruthi
INPUT: Reading input from 'cluster.in'
[parm noions.prmtop]
Reading 'noions.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin gamd2.nc]
Reading 'gamd2.nc' as Amber NetCDF
[loadcrd gamd2.nc 1 last 5 clus_crd]
Reading 'gamd2.nc' as Amber NetCDF
Warning: COORDS data sets do not store times.
Loading trajectory 'gamd2.nc' as 'clus_crd'
----- gamd2.nc (1-250000, 5) -----
[cluster hieragglo epsilon 3 clusters 10 averagelinkage rms :1-1362 mass
sieve 10 out clus_out.dat summary clus_summary.dat info clus_info3.dat
repout rep3 repfmt pdb]
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask
[:1-1362]), mass-weighted best-fit
Hierarchical Agglomerative: 10 clusters, epsilon 3.000, average-linkage.
Sieved frames will not be included in final cluster distance calculation.
Initial clustering sieve value is 10 frames.
Only non-sieved frames will be used to calc within-cluster average.
Cluster # vs time will be written to clus_out.dat
Pairwise distance data set is 'Cnum_00003[PWD]'
Cluster information will be written to clus_info3.dat
Summary of cluster results will be written to clus_summary.dat
Representative frames will be chosen by closest distance to cluster
centroid.
Cluster representatives will be written to separate trajectories,
prefix (rep3), format PDB
Warning: One or more analyses requested creation of default COORDS DataSet.
CREATECRD: Saving coordinates from Top noions.prmtop to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: noions.prmtop, 27735 atoms, 1530 res, box: Orthogonal, 7 mol
INPUT TRAJECTORIES (1 total):
0: 'gamd2.nc' is a NetCDF AMBER trajectory with coordinates, time, box,
Parm noions.prmtop (Orthogonal box) (reading 250000 of 250000)
Coordinate processing will occur on 250000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noions.prmtop' (1 actions):
0: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store times.
Estimated memory usage (250000 frames): 83.211 GB
----- gamd2.nc (1-250000, 1) -----
0% 10% Killed
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 22 2021 - 07:00:03 PDT
