Molecular Dynamics Simulation Trajectory Data of Adsorption Induced Phase Transformation of a MOF Nanocrystallite

Overview In an in silico adsorption experiment, the closed pore nanoscrystallite (NC) DUT-8(Cu) (9x9x9 Paddle wheel units) was embedded in a reservoir of 44000 CO2 molecules. At a temperature of 300 K and a pressure of 30 bar the system was simulated using the MOF-FF force field for 5 ns. Without any bias the NC opens up and adsorbs about 12 CO2 per pore, doubling its volume. Simulations have been performed using LAMMPS with our pylmps wrapper, which generates LAMMPS-input files on the fly. pylmps can be found in https://github.com/MOFplus/cmc-tools. Three independent runs have been performed. In the corresponding publication, mainly the first run (r0) was analyzed in detail. Content Here the slightly condensed full trajectories of all three runs are published as mfp5 files, es produced by pylmps/LAMMPS. The mfp5 file is a structured hdf5 file and can be read and browsed by any hdf5 viewer or using the h5py library in Python. The MD simulation was performed with a timestep of 1 fs and trajectory frames were written every 100 steps. In order to reduce the filesize, only the production stages with a stride of 10 frames are included. Each trajectory file thus contains 5000 steps with a frequency of 1 ps. For each trajectory a video using again every 10th frame (500 frames with 24 frames/sec) with a top view down the z-axis (including all atoms and the simulation cell) is included as a preview. The structure of the mfp5 file (which includes also the system and force field information) is explained in mfp5_file_structure.pdf. Due to processing, the table_name attributes for the thermodynamic data in the thermo dataset within the mfp5 files have been lost. For clarity, the headings are given here explicit:Step E_vdwl E_coul E_long E_bond E_angle E_impro E_dihed PotEng KinEng TotEng Temp Press Volume Cella Cellb Cellc CellAlpha CellBeta CellGamma Pxx Pyy Pzz Pxy Pxz Pyz S/CPUIn simulation_input.zip the starting structure and force field definition for pylmps are given as a mfpx/ric/par file triple. The mfpx file is a coordinate file with atomtypes, fragmentname/number information and the connectivity. The par file contains the force field definition and paramters and the ric file gives all bonds, angles, torsions and out-of-plane bonded interactions using atom indices and an integer reference to the par file. Note, that pylmps produces LAMMPS input files (in and data) on the fly from these, whcih are also included for clarity.