Updates of the GROMOS Software

GROMOS 11 MD++ version 1.6.1 (April 2024)

Bug fixes:

• The timing of parallel code occasionally led to segmentation faults due to a race condition
• Minor bug fix in the REEDS code
• Minor bug fix in the periodic local elevation code

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GROMOS 11 version 1.6.0 (November 2023)

New functionalities:

• Support for virtual atoms with nonbonded interactions.
• Shifted reaction-field [1].
• Buffer region Neural Network [2].
• Combined TI with (A-)EDS [3].
• Selective Gaussian accelerated MD [4].

References:

1. A. Kubincova, S. Riniker, P.H. Hünenberger, Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff, Phys. Chem. Chem. Phys. 22 (2020) 26419-26437, doi: 10.1039/d0cp03835k
2. B. Lier, P. Poliak, P. Marquetand, J. Westermayr, C. Oostenbrink, BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations, J. Phys. Chem. Lett 13 (2022) 3812−3818, doi: 10.1021/acs.jpclett.2c00654
3. O. Gracia Carmona, M. Gillhofer, L. Tomasiak, A. de Ruiter, C. Oostenbrink, Accelerated enveloping distribution sampling to probe the presence of water molecules, J. Chem. Theory Comput. 19 (2023) 3379–3390, doi: 10.1021/acs.jctc.3c00109
4. O. Gracia Carmona and C. Oostenbrink, Flexible Gaussian accelerated molecular dynamics to enhance biological sampling, J. Chem. Theory Comput. 19 (2023) 6521–6531, doi: 10.1021/acs.jctc.3c00619

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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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GROMOS 11 version 1.4.0 (February 2018)

New functionalities:

• Extended TI [1].
• Improved reading and checking of input parameters.
• Speedup of pairlisting and nonbonded interactions.
• Extension of tutorial and manual.

References:

1. A. de Ruiter, C. Oostenbrink, Extended thermodynamic integration: Efficient prediction of lambda derivatives at nonsimulated points, J. Chem. Theory Comput. 12 (2016) 4476-4486, doi: 10.1021/acs.jctc.6b00458

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GROMOS 11 version 1.3.0 (May 2016)

New functionalities:

• Polarisable force-field code [1].
• Order-parameter restraining [2].
• Distance-field restraining [3].
• Coarse-grained models [4].

References:

1. S.J. Bachmann, W.F. van Gunsteren, On the compatibility of polarisable and non-polarisable models for liquid water, Mol. Phys. 112 (2014) 2761-2780, doi: 10.1080/00268976.2014.910317
2. N. Hansen, F. Heller, N Schmid, W.F. van Gunsteren, Time-averaged order parameter restraints in molecular dynamics simulations, J. Biomol. NMR 60 (2014) 169-187, doi: 10.1007/s10858-014-9866-7
3. A. de Ruiter, C. Oostenbrink, Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations, J. Chem. Theory Comput. 9 (2013) 883-892, doi: 10.1021/ct300967a
4. S. Riniker, J.R. Allison, W.F. van Gunsteren, On developing coarse-grained models for biomolecular simulation: a review, Phys. Chem. Chem. Phys. 14 (2012) 12423-12430, doi: 10.1039/C2CP40934H

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Addition of new force-field files (November 18, 2015)

• Checked new 56a6@CARBO-R files into official ff directory. 56a6@CARBO-R is a revision of 56a6@CARBO. The force-field changes are limited (one torsion and one type of LJ exceptions). However, this small change has a large impact on the ring conformational properties of O1-methlyated hexopyranoses and hexopyranoses within chains (no effect on free hexopyranoses).

References:

• W. Plazinski, A. Lonardi, and P.H. Hunenberger, Revision of the GROMOS 56A6CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains, J Comput. Chem. 37 (2016) 354-365, doi: 10.1002/jcc.24229

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Changes in force-field files (May 24, 2013)

• Correction of galactose torsion in 53A5 and later ifp files. Dihedral angle type 37 had an incorrect force constant of 4.97 instead of 6.66. This has no effect on the carbohydrate force field 56A6@CARBO, which does not use this dihedral.

• Update of beta peptides mtb files. Restored the dihedral types 39 and 40 for phi and psi, respectively, in beta-peptides, in replacement to the types 43 and 44 for phi and 42 and 45 for psi; i.e. beta-peptides in 54A7(8) have now the same phi and psi parameters as alpha- and beta-peptides in 53A6, which differ from those of alpha-peptides in 54A7(8). As a consequence the files 54a7(8)_beta.mtb from before May 13, 2013 are different from the current files.

• Addition of special N-termini for alpha- and beta-amino acids. New N-terminal patches GH3+ and GH2 for alpha-peptides; these are meant to precede a residue where CA is a CH2 united atom (for natural aminoacids, this is only glycine; for CH1 united atom, use NH3+ and NH2 instead). New N-terminal patches AH3+ and AH2 for beta-peptides; these are meant to precede a residue where CB is a CH2 united atom (for CH1 united atom, use BH3+ and BH2 instead).

• Addition of post-translational modified amino acids, see [1,2]. Building blocks compatible with the 54A7 force field can be found in the file 54a7_ptm.mtb. Building blocks compatible with the 45a3 force field can be found in the file 45a3.mtb.

References:

1. C. Margreitter, D. Petrov, and B. Zagrovic, Vienna-PTM webserver: a toolkit for MD simulations of protein post-translational modifications, Nucleic Acid. Res. 41 (2013) W423, doi: 10.1093/nar/gkt416
2. D. Petrov, C. Margreitter, M. Grandits, C. Oostenbrink, and B. Zagrovic, Development and verification of force-field parameters for molecular dynamics simulations of protein post-translational modifications, PLOS Comput. Biol. 9 (2013) e1003154, doi: 10.1371/journal.pcbi.1003154

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GROMOS11 version 1.2.0 (September 2012)

New functionalities:

• QM/MM interface [1]
• Twin-system EDS [2]
• New replica-exchange implementation for MPI

New force-field files:

• 54A8 [3], 56A6@CARBO [4]
• New cofactor files 54c7_cof.mtb, 54d7_cof.mtb, 54c8_cof.mtb: Charge distributions for cofactors in the C(D) parameter sets are updated from the 43A(B)1 charge distributions according to analogy with charge distributions in similar functional groups in the corresponding A(B) parameter set. E.g. an OH-group in a cofactor in 54A(B)7 has the original 43A(B)1 charge distribution, while an OH-group in a cofactor in 54C(D)7 has a similar charge distribution as an OH-group in the peptide parameters of the 54A(B)7 parameter set. These files were not specifically tested.

Functions no longer supported:

• The GROMOS96COMPAT block was removed. To allow the reproduction of results that have been obtained using the GROMOS96COMPAT block, i.e. without contributions from excluded 1-2, 1-3 and self-interaction terms to the energy [5], a new switch (NSLFEXCL) has been introduced in the NONBONDED block. However, we strongly recommend to use the default reaction field formalism [6] (NSLFEXCL=1) that includes the 1-2, 1-3 and self-interaction terms.
• The multi-graining program was removed. The new GROMOS version allows for three coarse graining options: 1) MARTINI CG, 2) pure GROMOS CG [7], 3) mixed GROMOS CG/FG [8].

References:

1. K. Meier, N. Schmid, and W. F. van Gunsteren, Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages, J. Comput. Chem. 33 (2012) 2108-2117, doi: 10.1002/jcc.23047
2. N. Hansen, P. H. Hünenberger, and W. F. van Gunsteren, Efficient combination of environment change and alchemical perturbation within the enveloping distribution sampling (EDS) scheme: Twin-system EDS and application to the determination of octanol-water partition coefficients, J. Chem. Theory Comput. 9 (2013) 1334-1346, doi: 10.1021/ct300933y
3. M. M. Reif, P. H. Hünenberger, and C. Oostenbrink, New interaction parameters for charged amino acid side chains in the GROMOS force field, J. Chem. Theory Comput. 8 (2012) 3705-3723, doi: 10.1021/ct300156h
4. H. Hansen and P. H. Hünenberger, A reoptimized GROMOS force field for hexapyranose-based carbohydrates accounting for relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers and glycosidic linkage conformers, J. Comput. Chem. 32 (2011) 998-1032, doi: 10.1002/jcc.21675
5. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag an der ETH Zürich, Zürich, Switzerland, 1996, p. II-30.
6. M. Christen, P. H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, and W. F. van Gunsteren, The GROMOS software for biomolecular simulation: GROMOS05, J. Comput. Chem. 26 (2005) 1719-1751, doi: 10.1002/jcc.20303
7. S. Riniker and W. F. van Gunsteren, A simple, efficient and polarizable coarse-grained water model for molecular dynamics simulations, J. Chem. Phys. 134 (2011) 084110, doi: 10.1063/1.3553378
8. S. Riniker, A. Eichenberger, and W. F. van Gunsteren, Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations, Eur. Biophys. J. 41 (2012) 647-661, doi: 10.1007/s00249-012-0837-1

GROMOS - Software for Biomolecular Simulation