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Release 1.5.0
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@oostenbrink oostenbrink released this 15 Apr 16:03
· 169 commits to master since this release
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GROMOS 11 version 1.5.0 (January 2021)

New functionalities:

  • Accelerated EDS [1].
  • Replica exchange EDS [2,3].
  • Improved dihedral-angle constraints [4].
  • Improved QM/MM options.
  • GPU acceleration [5] now embedded in main md++ package.
  • Simplified calculation of post-MD corrections for charge-changing free-energy calculations [6].

Along with this release a suite of advanced tutorials was published covering NMR order parameter restraining as well as binding free energy calculations involving a charged ligand [7].

References:

  1. J. W. Perthold, C. Oostenbrink, Accelerated enveloping distribution sampling: Enabling sampling of multiple end-states while preserving local minima, J. Phys. Chem. B 122 (2018) 5030-5037, doi: 10.1021/acs.jpcb.8b02725
  2. D. Sidler, A. Schwaninger, S. Riniker, Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation, J. Chem. Phys. 145 (2016) 154114, doi: 10.1063/1.4964781
  3. D. Sidler, M. Cristòfol-Clough, S. Riniker, Efficient round-trip optimization for replica-exchange enveloping distribution sampling (RE-EDS), J. Chem. Theory Comput. 13 (2017) 3020-3030, doi: 10.1021/acs.jctc.7b00286
  4. M. Pechlaner, W. F. van Gunsteren, Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations, J. Chem. Phys. 152 (2020) 024109, doi: 10.1063/1.5124923
  5. N. Schmid, M. Bötschi, W. F. van Gunsteren, A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software, J. Comput. Chem. 31 (2010) 1636-1643, doi: 10.1002/jcc21447
  6. C. Öhlknecht, B. Lier, D. Petrov, J. Fuchs, C. Oostenbrink, Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies, J. Comput. Chem. 41 (2020) 986-999, doi: 10.1002/jcc.26143
  7. B. Lier, C. Öhlknecht, A. de Ruiter, J. Gebhardt, W. F. van Gunsteren, C. Oostenbrink, N. Hansen, A suite of advanced tutorials for the GROMOS biomolecular simulation software [article v1.0], Living J. Comp. Mol. Sci. 2 (2020) 18552, doi: 10.33011/livecoms.2.1.18552
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