Closed hainm closed 8 years ago
full log for case 2
CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 10/09/15 00:20:15
| Available memory: 508.012 MB
INPUT: Reading Input from file tz2.hbond.in
[parm tz2.ortho.parm7]
Reading 'tz2.ortho.parm7' as Amber Topology
[trajin tz2.ortho.nc]
Reading 'tz2.ortho.nc' as Amber NetCDF
[hbond image out hb.dat]
HBOND: Searching for Hbond donors/acceptors in region specified by *
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing # Hbond v time results to hb.dat
Imaging enabled.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'tz2.ortho.parm7', 5293 atoms, 1704 res, box: Orthogonal, 1692 mol, 1691 solvent, 10 frames
INPUT TRAJECTORIES:
0: 'tz2.ortho.nc' is a NetCDF AMBER trajectory, Parm tz2.ortho.parm7 (Orthogonal box) (reading 10 of 10)
Coordinate processing will occur on 10 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'tz2.ortho.parm7' (1 actions):
0: [hbond image out hb.dat]
Set up 38 acceptors:
Set up 31 donors:
Imaging on.
Estimated max potential memory usage: 0.09 MB
----- tz2.ortho.nc (1-10, 1) -----
0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.
Read 10 frames and processed 10 frames.
TIME: Trajectory processing: 0.0186 s
TIME: Avg. throughput= 537.2300 frames / second.
ACTION OUTPUT:
HBOND: Actual memory usage is 0.00 MB
0 solute-solute hydrogen bonds.
DATASETS:
2 data sets:
tz2.ortho.parm7 "tz2.ortho.parm7" (topology), size is 5293 'tz2.ortho.parm7', 5293 atoms, 1704 res, box: Orthogonal, 1692 mol, 1691 solvent
HB_00001[UU] "HB_00001[UU]" (integer), size is 10
DATAFILES:
hb.dat (Standard Data File): HB_00001[UU]
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0673 seconds.
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To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
Fixed by #107, thanks for the report.
I was trying to use image on/off but got 0 hbond with image on
case 1
output
case 2
output
according to this topic http://archive.ambermd.org/201506/0455.html, is 'image' in hbond similiar to
autoimage
? if yes, why the output in two cases are so different?