General
Usage
The trajectory analysis tool is automatically called when a trajectory is loaded using the -f flag.
As a first step, the program identifies and characterizes all rigid structures in the trajectory by comparing the first two frames of the trajectory and identifying all frozen atoms.
The structures must therefore remain frozen throughout the simulation.
Optionally, the user can manually define a structure with the -m flag.
This is helpful if some structures are moving or flexible, or when some structures are frozen, while others are not.
$ CONAN -f <trajectoryfile> -m -i inp
Note
The trajectory must be in either .xyz, .pdb or LAMMPS (.lammpstrj or .lmp) format.
If the trajectory is in xyz format, the user will be prompted to enter the simulation box dimensions, which are required for some analyses.
In the case of the pdb and LAMMPS formats, the box dimensions are read directly from the trajectory.
Molecule identification
The program includes a molecule identifier that detects all bonds between atoms based on distance criteria. The cutoff distances, which determine whether two atoms are bonded, vary depending on the elements involved. These element combinations and their corresponding cutoff distances are detailed in a library. The program analyzes the first frame of the trajectory to identify all molecules, meaning it does not account for bond breaking or formation throughout the trajectory. Periodic boundary conditions are taken into consideration during this process. Once molecules are recognized, the program outputs the number of unique molecules and their respective quantities within the system. Additionally, it generates images of the identified molecules (for those with fewer than 50 atoms) complete with atom labels.
Parameters
The following parameters may be required for the implemented analysis options
Element Masses
Number of increments (user defined)
Note
For all analysis options the listed atomic masses are used. If the user wants to use different masses, they have to be added in defdict.py.
Note
The user is asked to choose between van der Waals radii and covalent radii.
Note
The masses and radii of Drude particles (D) and dummy atoms (X) are set to zero.
element |
mass [u] |
vdW radius [Å] |
covalent radius [Å] |
|---|---|---|---|
H |
1.008 |
1.20 |
0.31 |
C |
12.011 |
1.70 |
0.76 |
N |
14.007 |
1.55 |
0.71 |
O |
15.999 |
1.52 |
0.66 |
F |
18.998 |
1.47 |
0.57 |
P |
30.974 |
1.80 |
1.07 |
S |
32.065 |
1.80 |
1.05 |
Li |
6.941 |
1.81 |
1.28 |
Na |
22.990 |
2.27 |
1.66 |
K |
39.098 |
2.75 |
2.03 |
Mg |
24.305 |
1.73 |
1.41 |
Ca |
40.078 |
2.31 |
1.76 |
B |
10.811 |
1.65 |
0.84 |
Ag |
107.868 |
1.72 |
1.45 |
Au |
196.967 |
1.66 |
1.36 |
D |
0.00 |
0.00 |
0.00 |
X |
1.00 |
0.00 |
0.00 |