- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Yinglong Miao <yimiao.ucsd.edu>

Date: Tue, 14 Jan 2020 10:05:11 -0600

Following is the entire cpptraj output:

CPPTRAJ: Trajectory Analysis. V4.15.0 (AmberTools V20.00)

___ ___ ___ ___

| \/ | \/ | \/ |

_|_/\_|_/\_|_/\_|_

| Date/time: 01/13/20 17:36:28

| Available memory: 7.793 GB

INPUT: Reading input from 'sys-clustering-dpeaks.cpptraj'

[parm APN.prmtop]

Reading 'APN.prmtop' as Amber Topology

Radius Set: modified Bondi radii (mbondi)

[trajin gamd-no-reimaged-ts10ps-lenns-APN.nc]

Reading 'gamd-no-reimaged-ts10ps-lenns-APN.nc' as Amber NetCDF

[cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg

runavg.dat deltafile delta.dat sieve 200]

CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (all

atoms) best-fit

---------------------------------------------------------------------------

Warning: The dpeaks algorithm is still under development. USE WITH CAUTION!

---------------------------------------------------------------------------

DPeaks: Cutoff (epsilon) for determining local density is 4

Discrete density calculation.

Density vs min distance to point with next highest density

written to dvdfile

Attempting to choose density peaks automatically.

Running avg of delta vs distance written to runavg.dat

Delta of distance minus running avg written to delta.dat

Initial clustering sieve value is 200 frames.

Only non-sieved frames will be used to calc within-cluster average.

Pairwise distance data set is 'C0[PWD]'

Representative frames will be chosen by closest distance to cluster

centroid.

[go]

Warning: One or more analyses requested creation of default COORDS DataSet.

CREATECRD: Saving coordinates from Top APN.prmtop to "_DEFAULTCRD_"

---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):

0: APN.prmtop, 15 atoms, 1 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):

0: 'gamd-no-reimaged-ts10ps-lenns-APN.nc' is a NetCDF AMBER trajectory

with coordinates, time, box, Parm APN.prmtop (Orthogonal box) (reading

250000 of 250000)

Coordinate processing will occur on 250000 frames.

BEGIN TRAJECTORY PROCESSING:

.....................................................

ACTION SETUP FOR PARM 'APN.prmtop' (1 actions):

0: [createcrd _DEFAULTCRD_]

Warning: COORDS data sets do not store times.

Estimated memory usage (250000 frames): 51.000 MB

----- gamd-no-reimaged-ts10ps-lenns-APN.nc (1-250000, 1) -----

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 250000 frames and processed 250000 frames.

TIME: Avg. throughput= 616579.0713 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:

0: [cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg

runavg.dat deltafile delta.dat sieve 200]

Starting clustering.

Mask [*] corresponds to 15 atoms.

Estimated pair-wise matrix memory usage: > 3.123 MB

Pair-wise matrix set up with sieve, 250000 frames, 1250 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: 4.128 MB

Starting DPeaks clustering, discrete density calculation.

Determining local density of each point.

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Finding closest neighbor point with higher density for each point.

0% 10% 20% 30% 40% 50% 60% 70% 80% 90%

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Segmentation fault (core dumped)

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jan 14 2020 - 08:30:02 PST

Date: Tue, 14 Jan 2020 10:05:11 -0600

Following is the entire cpptraj output:

CPPTRAJ: Trajectory Analysis. V4.15.0 (AmberTools V20.00)

___ ___ ___ ___

| \/ | \/ | \/ |

_|_/\_|_/\_|_/\_|_

| Date/time: 01/13/20 17:36:28

| Available memory: 7.793 GB

INPUT: Reading input from 'sys-clustering-dpeaks.cpptraj'

[parm APN.prmtop]

Reading 'APN.prmtop' as Amber Topology

Radius Set: modified Bondi radii (mbondi)

[trajin gamd-no-reimaged-ts10ps-lenns-APN.nc]

Reading 'gamd-no-reimaged-ts10ps-lenns-APN.nc' as Amber NetCDF

[cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg

runavg.dat deltafile delta.dat sieve 200]

CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (all

atoms) best-fit

---------------------------------------------------------------------------

Warning: The dpeaks algorithm is still under development. USE WITH CAUTION!

---------------------------------------------------------------------------

DPeaks: Cutoff (epsilon) for determining local density is 4

Discrete density calculation.

Density vs min distance to point with next highest density

written to dvdfile

Attempting to choose density peaks automatically.

Running avg of delta vs distance written to runavg.dat

Delta of distance minus running avg written to delta.dat

Initial clustering sieve value is 200 frames.

Only non-sieved frames will be used to calc within-cluster average.

Pairwise distance data set is 'C0[PWD]'

Representative frames will be chosen by closest distance to cluster

centroid.

[go]

Warning: One or more analyses requested creation of default COORDS DataSet.

CREATECRD: Saving coordinates from Top APN.prmtop to "_DEFAULTCRD_"

---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):

0: APN.prmtop, 15 atoms, 1 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):

0: 'gamd-no-reimaged-ts10ps-lenns-APN.nc' is a NetCDF AMBER trajectory

with coordinates, time, box, Parm APN.prmtop (Orthogonal box) (reading

250000 of 250000)

Coordinate processing will occur on 250000 frames.

BEGIN TRAJECTORY PROCESSING:

.....................................................

ACTION SETUP FOR PARM 'APN.prmtop' (1 actions):

0: [createcrd _DEFAULTCRD_]

Warning: COORDS data sets do not store times.

Estimated memory usage (250000 frames): 51.000 MB

----- gamd-no-reimaged-ts10ps-lenns-APN.nc (1-250000, 1) -----

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 250000 frames and processed 250000 frames.

TIME: Avg. throughput= 616579.0713 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:

0: [cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg

runavg.dat deltafile delta.dat sieve 200]

Starting clustering.

Mask [*] corresponds to 15 atoms.

Estimated pair-wise matrix memory usage: > 3.123 MB

Pair-wise matrix set up with sieve, 250000 frames, 1250 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: 4.128 MB

Starting DPeaks clustering, discrete density calculation.

Determining local density of each point.

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Finding closest neighbor point with higher density for each point.

0% 10% 20% 30% 40% 50% 60% 70% 80% 90%

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.

Segmentation fault (core dumped)

-- You can find a copy of the dvdfile as attached. I will try the gauss option to see how it works ... Thank you, Yinglong On Tue, Jan 14, 2020 at 9:47 AM Daniel Roe <daniel.r.roe.gmail.com> wrote: > Can you provide me (either in reply to this or off list) your entire > cpptraj output and the contents of dvdfile? > > This could happen with very sparse density I think, although its > difficult to say without exactly replicating. You could potentially > try the 'gauss' keyword for Gaussian density instead of discrete > density. > > -Dan > > On Mon, Jan 13, 2020 at 8:10 PM Yinglong Miao <yinglong.miao.gmail.com> > wrote: > > > > Hi Dan, > > > > Itâ€™s the latest version as in AMBER git repository. > > > > Thanks, > > Yinglong > > > > > > > On Jan 13, 2020, at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > > > > > What version of cpptraj are you using? > > > > > > -Dan > > > > > > On Mon, Jan 13, 2020 at 6:51 PM <yinglong.miao.gmail.com> wrote: > > >> > > >> Hello, > > >> > > >> I tried to use the dpeaks algorithm for clustering with the following > > >> command: > > >> cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg > > >> runavg.dat deltafile delta.dat sieve 200 > > >> > > >> But keep getting the following output with error: > > >> ... > > >> Finding closest neighbor point with higher density for each point. > > >> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% > > >> Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor > is -1. > > >> Segmentation fault (core dumped) > > >> > > >> I will appreciate any suggestions that would fix this ... > > >> > > >> Thanks, > > >> Yinglong > > >> > > >> Yinglong Miao, Ph.D. > > >> Assistant Professor > > >> Center for Computational Biology and > > >> Department of Molecular Biosciences > > >> University of Kansas > > >> http://miao.compbio.ku.edu > > >> _______________________________________________ > > >> AMBER mailing list > > >> AMBER.ambermd.org > > >> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber >

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

- application/octet-stream attachment: dvdfile

Custom Search