CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 04/19/16 10:33:44
| Available memory: 16.125 GB
INPUT: Reading input from 'pt-hb-wat.in'
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
[autoimage origin]
Warning: Action specified before trajin/ensemble. Assuming trajin.
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,]
Reading '../../traj.1.01' as Amber NetCDF
[hbond nointramol solvout avghb-wat.dat solventdonor :WAT acceptormask :1-2 printatomnum dist 3 printatomnum]
HBOND: Acceptor mask is :1-2, donors will be searched for in a region specified by *
Only looking for intermolecular hydrogen bonds.
Will search for hbonds between solute and solvent donors in [:WAT]
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing solute-solvent hbond avgs to avghb-wat.dat
Writing solvent bridging info to avghb-wat.dat
Atom numbers will be written to output.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (1 total):
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
Looking for frames at 298.41 K
Coordinate processing will occur on 50000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (2 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [hbond nointramol solvout avghb-wat.dat solventdonor :WAT acceptormask :1-2 printatomnum dist 3 printatomnum]
Set up 65 acceptors:
Set up 8 donors:
Set up 2150 solvent donors
Imaging off.
Estimated max potential memory usage: 45.068 kB
----- traj.1.01 (1-50000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Avg. throughput= 103.5651 frames / second.
ACTION OUTPUT:
HBOND: Actual memory usage is 4.880 kB
0 solute-solute hydrogen bonds.
63 solute-solvent hydrogen bonds.
1 unique solute-solvent bridging interactions.
DATASETS (4 total):
printatomnum[UU] "printatomnum[UU]" (integer), size is 50000
printatomnum[UV] "printatomnum[UV]" (integer), size is 50000
printatomnum[Bridge] "printatomnum[Bridge]" (integer), size is 50000
printatomnum[ID] "printatomnum[ID]" (string), size is 50000
DATAFILES (1 total):
avghb-wat.dat (Avg. solute-solvent HBonds, Solvent bridging info)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 482.7881 s ( 99.94%)
TIME: Action Post : 0.2802 s ( 0.06%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 483.0685 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 507.2849 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.