MD simulation of the crystal unit cell of the second PDZ domain of LNX2 protein

This molecular dynamics simulation data is provided as part of the manuscript "LAWS: Local Alignment for Water Sites - a method to analyze crystallographic water in simulations". The code for the algorithm is provided: on github The system contains one unit cell of the crystal (PDB ID: 5E11) with 4 symmetrically related protein chains. The total simulation length is 1 microsecond. Force field + water model: CHARMM36m + CHARMM-modified TIP3P Number of atoms: 9650 Number of time frames: 100,000 with 10-ps stride The details of the simulations are provided in the manuscript.

Related Organizations

University of Toronto
Canada

Keywords

md simulations, crystal, protein crystal

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