Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

  title={Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset},
  author={Michael R. Shirts and Christoph Klein and Jason M. Swails and Jian Yin and Michael K. Gilson and David L. Mobley and David A. Case and Ellen D. Zhong},
  journal={Journal of Computer-Aided Molecular Design},
We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find… 

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