Gromacs

Implicit Solvent

    Table of contents
    1. 1. References

    With the release of GROMACS version 4.5, it is possible to conduct simulations using implicit solvent models.  See the manual, section 3.18, for the options related to implicit solvent calculations.  Currently, the generalized-Born formalism is used and there are three methods available for the calculation of Born radii: 

    • Still
    • Hawkins-Cramer-Truhlar (HCT)
    • Onufriev-Bashford-Case (OBC)

    For the details of these methods, see the references linked below.  Over the last few years there have been quite a few papers in (good) journals about why one in general should or should not use implicit solvent.  These papers are also linked below.

     

    References

    1. D. Qui, P. Shenkin, F. Hollinger, and W. Still. (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A. 101 (16): 3005-3014. DOI
    2. D. Hawkins, C. Cramer, and D. Truhlar. (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100 (51): 19824-19839. DOI
    3. A. Onufriev, D. Case, and D. Bashford. (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55 (2): 383-394. DOI
    4. R. Zhou and B. J. Berne. (2002) Can a continuum solvent model reproduce the free energy landscape of a β-hairpin in water? Proc. Natl. Acad. Sci. U.S.A. 99: 12777-12782. DOI
    5. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, and V. S. Pande. (2004) Simulations of the role of water in the protein- folding mechanism. Proc. Natl. Acad. Sci. U.S.A. 101: 6456-6461. DOI
    6. H. Fan, A. E. Mark, J. Zhu, and B. Honig. (2005) Comparative study of generalized Born models: protein dynamics. Proc. Natl. Acad. Sci. U.S.A. 102: 6760-6764. DOI
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