This package is a little tool to handle gromacs/lammps/pdb trajectory files, with pandas and numpy. This allows:
- Straight-forward and easy manimpulation of atoms, selecting by residue name, atom name, id, x, y, z, etc, within pandas data frame;
- Faster statistical calculations for thousands of frames by vectorization (numpy array calc).
This package can be used to:
- reads and export lammps trj, gro and pdb (unwrapped gro and pbc) into/from pandas data frame (only orthogonal box),
- generates ions by centers of mass.
- calculates association of the counterions (AN) and categorizes hopping types of the counterions (AN).
- calcualtes non gaussian parameter and mean square displacement for AN.
- calculates van hove function and distribution of string like motions for AN.
- calculates continous time autocorrelation function, intermittent time autocorrelation function, tau_c and tau_s.
- Fs(q,t) and tau_q
- saves trj in lammps format
- way more things to do!
Not completed yet but already useful.
Howto:
pdb.main_.py is the 'template'. gro.main_.py is the 'template'.
Please cite:
Luo, X.; Liu, H.; Paddison, S.J.; Molecular Dynamics Simulations of Polymerized Ionic Liquids: Mechanism of Ion Transport with Different Anions, ACS Appl. Polym. Mater. 2021, 3, 1, 141–152