Updates of the GROMOS Software
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 [8,9].
More details concerning additional changes and bug fixes are visible in the download section (after registration).
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.
- [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, submitted.
- [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. (2012) 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.
- [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.
- [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.
- [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.