MD Trajectory of the NH2-POA polymer in CH2Cl2

Published: 20 May 2020| Version 1 | DOI: 10.17632/k4nb4z3ff5.1
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 folds in a nonpolar solvent like dichloromethane. The folding is primarily driven by hydrogen bonding. 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 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.


University of Vermont


Molecular Dynamics