MD Trajectory for the [NH2-POA@Tet-1] complex in CH2Cl2

Published: 20-05-2020| Version 1 | DOI: 10.17632/69x74bkdb5.1
Severin Schneebeli


As described in our corresponding paper (DOI: 10.1016/j.chempr.2020.05.011), this MD trajectory shows that the NH2-POA polymer stretches out somewhat when binding to Tet-1 in a nonpolar solvent like dichloromethane. The trajectory is the last 400 ns of an 800-ns production run. For the sake of size constraints, it has been sliced to every fourth frame. It is provided in the Desmond file format (compatible with VMD).


Steps to reproduce

The MD simulation trajectory was obtained with the OPLS3 force field in explicit CH2Cl2 solvent in the NPT ensemble (300 K, 1 atm, Martyna-Tuckerman-Klein coupling scheme). All simulations were performed in the Maestro-Desmond program (GPU version 5.4) with a time step of 2 fs. The Ewald technique was used for the electrostatic calculations. The Van der Waals and short-range electrostatics were cut off at 9 Å. Hydrogen atoms were constrained using the SHAKE algorithm. MD trajectory was analyzed using in-house python scripts and the Schrödinger (2018-2 release) API.