Note: FixSol solvation model and FIXPVA2 tessellation scheme.

The FixSol conductorlike solvation model and the fixed points with variable areas (FIXPVA2) surface tessellation scheme are described. In the FixSol model, the singularity of the surface charge interaction is avoided by introducing a soft-core potential. The use of soft-core potential allows for the use of the FIXPVA2 scheme to partition the molecular surface into tesserae with desirable areas. The FixSol model is used together with biological force field to perform molecular dynamics simulation for proteins and DNA molecules in solution.

[1]  Jacopo Tomasi,et al.  A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics , 1997 .

[2]  T. Halgren.  MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular‐interaction energies and geometries , 1999, Journal of computational chemistry.

[3]  Christian Silvio Pomelli,et al.  A tessellationless integration grid for the polarizable continuum model reaction field , 2004, J. Comput. Chem..

[4]  Christian Griesinger,et al.  2-Aminopurine incorporation perturbs the dynamics and structure of DNA. , 2010, Angewandte Chemie.

[5]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[6]  V. Barone,et al.  Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .

[7]  J. W. Neidigh,et al.  Designing a 20-residue protein , 2002, Nature Structural Biology.

[8]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[9]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[10]  Hui Li,et al.  Excited state geometry of photoactive yellow protein chromophore: a combined conductorlike polarizable continuum model and time-dependent density functional study. , 2010, The Journal of chemical physics.

[11]  Martin Karplus,et al.  A Smooth Solvation Potential Based on the Conductor-Like Screening Model , 1999 .

[12]  Hui Li,et al.  Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation. , 2011, The Journal of chemical physics.

[13]  Hui Li,et al.  Continuous and smooth potential energy surface for conductorlike screening solvation model using fixed points with variable areas. , 2009, The Journal of chemical physics.

[14]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[15]  Michel Dupuis,et al.  Implementation of solvent reaction fields for electronic structure , 2002 .

[16]  Iñaki Tuñón,et al.  GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent‐excluding surface , 1994, J. Comput. Chem..

[17]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .