refs.bib

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@Article{Aqvist1990,
  Title                    = {Ion-water interaction potentials derived from free energy perturbation simulations},
  Author                   = {Aqvist, J.},
  Journal                  = {Journal of Physical Chemistry},
  Year                     = {1990},

  Month                    = {Oct},
  Number                   = {21},
  Pages                    = {8021–8024},
  Volume                   = {94},

  Doi                      = {10.1021/j100384a009},
  ISSN                     = {0022-3654},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/j100384a009}
}

@Article{Banas2010,
  Title                    = {Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins},

  Author                   = {Banas},
  Journal                  = {Journal of Chemical Theory and Computation},
  Year                     = {2010},
  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {3836–3849},
  Volume                   = {6},
  Doi                      = {10.1021/ct100481h},
  ISSN                     = {1549-9618},
  Publisher                = { American Chemical Society},
}

@Article{Basham1995,
  Title                    = {An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA.},
  Author                   = {Basham, B and Schroth, G P and Ho, P S and Rich, A.},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1995},

  Month                    = {Jul},
  Number                   = {14},
  Pages                    = {6464–8},
  Volume                   = {92},

  Doi                      = {10.1073/pnas.92.14.6464},
  ISSN                     = {0027-8424},
  Publisher                = {National Academy of Sciences},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/7604014}
}

@Article{Bergonzo2015,
  Title                    = {Improved Force Field Parameters Lead to a Better Description of RNA Structure.},
  Author                   = {Bergonzo, Christina and Cheatham 3rd, Thomas. E.},
  Journal                  = {Journal of chemical theory and computation},
  Year                     = {2015},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {3969–72},
  Volume                   = {11},

  Abstractnote             = {We compare the performance of two different RNA force fields in four water models in simulating the conformational ensembles r(GACC) and r(CCCC). With the increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data to evaluate force field reliability. The combination of AMBER ff12 with vdWbb modifications and the OPC water model produces results in quantitative agreement with the NMR ensemble that have eluded us to date.},
  Doi                      = {10.1021/acs.jctc.5b00444},
  ISSN                     = {1549-9626},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/acs.jctc.5b00444}
}

@Article{Bhattacharyya2016,
  Title                    = {Metal Cations in G-Quadruplex Folding and Stability.},
  Author                   = {Bhattacharyya, Debmalya and Mirihana Arachchilage, Gayan and Basu, Soumitra},
  Journal                  = {Frontiers in chemistry},
  Year                     = {2016},
  Pages                    = {38},
  Volume                   = {4},

  Abstractnote             = {This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.},
  Doi                      = {10.3389/fchem.2016.00038},
  ISSN                     = {2296-2646},
  Publisher                = {Frontiers Media SA},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/27668212}
}

@Article{Case2005,
  Title                    = {The Amber biomolecular simulation programs.},
  Author                   = {Case, D. A. and Cheatham 3rd, Thomas. E. and Darden, T. and Gohlke, H. and Luo, R. and Merz, K. M. and Onufriev, A. and Simmerling, C. and Wang, B. and Woods, R. J.},
  Journal                  = {Journal Of Computational Chemistry},
  Year                     = {2005},

  Month                    = {Dec},
  Number                   = {16},
  Pages                    = {1668–1688},
  Volume                   = {26},

  Abstractnote             = {We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.},
  Doi                      = {10.1002/jcc.20290},
  ISSN                     = {0192-8651},
  Url                      = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1989667&tool=pmcentrez&rendertype=abstract}
}

@InBook{Cheatham3rd2006,
  Title                    = {Using AMBER to simulate DNA and DNA},
  Author                   = {Cheatham 3rd, Thomas. E. and Case, D. A.},
  Chapter                  = {2},
  Editor                   = {Sponer, J. and Lankaš, F.Editors},
  Pages                    = {45–72},
  Publisher                = {Springer Netherlands},
  Year                     = {2006},

  Booktitle                = {Computational Studies of DNA and RNA}
}

@Article{Cheatham3rd2013,
  Title                    = {Twenty-five years of nucleic acid simulations.},
  Author                   = {Cheatham 3rd, Thomas. E. and Case, D. A.},
  Journal                  = {Biopolymers},
  Year                     = {2013},

  Month                    = {Jun},
  Pages                    = {969–977},
  Volume                   = {12},

  Abstractnote             = {We present a brief, and largely personal, history of computer simulations of DNA and RNA oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both explicit and implicit solvent models are described, and methods for estimating structures, thermodynamics and mechanical properties of duplexes are illustrated. This overview, covering about two decades of work, provides a perspective for a discussion of prospects and obstacles for future simulations of RNA and DNA.},
  Doi                      = {10.1002/bip.22331},
  ISSN                     = {0006-3525},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/23784813}
}

@Article{Cheatham3rd1999,
  Title                    = {A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.},
  Author                   = {Cheatham 3rd, Thomas. E. and Cieplak, P. and Kollman, P. A.},
  Journal                  = {Journal of Biomolecular Structure \& Dynamics},
  Year                     = {1999},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {845–862},
  Volume                   = {16},

  Abstractnote             = {We have examined some subtle parameter modifications to the Cornell et al. force field, which has proven quite successful in reproducing nucleic acid properties, but whose C2’-endo sugar pucker phase and helical repeat for B DNA appear to be somewhat underestimated. Encouragingly, the addition of a single V2 term involving the atoms C(sp3)-O-(sp3)-C(sp3)-N(sp2), which can be nicely rationalized because of the anomeric effect (lone pairs on oxygen are preferentially oriented relative to the electron withdrawing N), brings the sugar pucker phase of C2’-endo sugars to near perfect agreement with ab initio calculations (W near 162 degrees). Secondly, the use of high level ab initio calculations on entire nucleosides (in contrast to smaller model systems necessitated in 1994-95 by computer limitations) lets one improve the chi torsional potential for nucleic acids. Finally, the O(sp3)-C(sp3)- C(sp3)-O(sp3) V2 torsional potential has been empirically adjusted to reproduce the ab initio calculated relative energy of C2’-endo and C3’-endo nucleosides. These modifications are tested in molecular dynamics simulations of mononucleosides (to assess sugar pucker percentages) and double helices of DNA and RNA (to assess helical and sequence specific structural properties). In both areas, the modified force field leads to improved agreement with experimental data.},
  Doi                      = {10.1080/07391102.1999.10508297},
  ISSN                     = {0739-1102},
  Publisher                = {Taylor \& Francis},
  Url                      = {http://dx.doi.org/10.1080/07391102.1999.10508297}
}

@Article{Cheatham3rd1997,
  Title                    = {A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions.},
  Author                   = {Cheatham 3rd, Thomas. E. and Crowley, M F and Fox, T and Kollman, Peter A.},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1997},

  Month                    = {Sep},
  Number                   = {18},
  Pages                    = {9626–30},
  Volume                   = {94},

  ISSN                     = {0027-8424},
  Publisher                = {National Academy of Sciences},
  Doi                      = {10.1073/pnas.94.18.9626}
}

@Article{Cheatham3rd1996,
  Title                    = {Observation of the A-DNA to B-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution},
  Author                   = {Cheatham 3rd, Thomas. E. and Kollman, P.A.},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {1996},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {434–444},
  Volume                   = {259},

  Abstractnote             = {A large challenge in molecular dynamics (MD) simulations of proteins and nucleic acids is to find the correct “experimental” geometry when a simulation is started a significant distance away from it. In this study, we have carried out four unrestrained ≈1 ns length MD trajectories in aqueous solution on the DNA duplex d(CCAACGTTGG)2, two beginning in a canonicalA-DNA structure and two beginning in a canonicalB-DNA structure. As judged by root-mean-squared coordinate deviations, average structures computed from all four of the trajectories converge to within ≈0.8 to 1.6 Å (all atoms) of each other, which is 1.3 to 1.7 Å (all atoms of the central six residues from each strand) and 3.1 to 3.6 Å (all atoms) away from theB-DNA-like X-ray structure reported for this sequence. To our knowledge, this is the first example of multiple nanosecond molecular dynamics trajectories with full representation of DNA charges, solvent and long range electrostatics that demonstrate both internal consistency (two different starting structures and four different trajectories lead to a consistent average structure) and considerable agreement with the X-ray crystal structure of this sequence and NMR data on duplex DNA in aqueous solution. This internal consistency of structure for a given sequence suggests that one can now begin to realistically examine sequence-dependent structural effects in DNA duplexes using molecular dynamics.},
  Doi                      = {10.1006/JMBI.1996.0330},
  ISSN                     = {0022-2836},
  Publisher                = {Academic Press}
}

@Article{Cornell1995,
  Title                    = {A second generation force field for the simulation of proteins, nucleic acids, and organic molecules},
  Author                   = {Cornell, W. D. and Cieplak, P. and Bayly, C. I. and Gould, I. R. and Merz, K. M. and Ferguson, D. M. and Spellmeyer, D. C. and Fox, T. and Caldwell, J. W. and Kollman, P. A.},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {1995},

  Month                    = {May},
  Number                   = {19},
  Pages                    = {5179–5197},
  Volume                   = {117},

  Doi                      = {10.1021/ja00124a002},
  ISSN                     = {0002-7863},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/ja00124a002}
}

@Article{Darden1993,
  Title                    = {Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems},
  Author                   = {Darden, T. A. and York, D. and Pedersen, L.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1993},
  Number                   = {12},
  Pages                    = {10089},
  Volume                   = {98},

  Doi                      = {10.1063/1.464397},
  ISSN                     = {00219606}
}

@Article{Drew1981,
  Title                    = {Structure of a B-DNA dodecamer: conformation and dynamics},
  Author                   = {Drew, H. R. and Wing, R. M. and Takano, T. and Broka, C. and Tanaka, S. and Itakura, K. and Dickerson, R. E.},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1981},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {2179–83},
  Volume                   = {78},

  ISSN                     = {0027-8424},
  PMID                     = {6914276}
}

@Article{Galindo-Murillo2016,
  Title                    = {Assessing the Current State of Amber Force Field Modifications for DNA},
  Author                   = {Galindo-Murillo, Rodrigo and Robertson, James C. and Zgarbová, Marie. and Šponer, Jiří. and Jurečka, Petr. and Cheatham 3rd, Thomas. E.},
  Journal                  = {Journal of Chemical Theory and Computation},
  Year                     = {2016},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {4114–4127},
  Volume                   = {12},

  Abstractnote             = {The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew–Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to assess and validate the current force fields and water models aggregate over 14 ms of simulation time. The results suggest that both the bsc1 and OL15 force fields render average structures that deviate significantly less than 1 Å from the average experimental structures. This can be compared to similar but less exhaustive simulations with the CHARMM 36 force field that aggregate to the ∼90 μs time scale and also perform well but do not produce structures as close to the DDD NMR average structures (…},
  Doi                      = {10.1021/acs.jctc.6b00186},
  ISSN                     = {15499626},
  Publisher                = {American Chemical Society},
  Url                      = {http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00186}
}

@Article{Galindo-Murillo2014,
  Title                    = {On the absence of intra-helical DNA dynamics on the micro to ms timescale},
  Author                   = {Galindo-Murillo, R. and Roe, Daniel R. and Cheatham 3rd, Thomas. E.},
  Journal                  = {Nature Communications},
  Year                     = {2014},

  Month                    = {Jan},
  Pages                    = {5152},
  Volume                   = {5},
  Doi                      = {10.1038/ncomms6152},
  ISSN                     = {2041-1723},
  Publisher                = {Nature Publishing Group},
}

@Article{Galindo-Murillo2014a,
  Title                    = {Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).},
  Author                   = {Galindo-Murillo, Rodrigo and Roe, Daniel R and Cheatham 3rd, Thomas. E.},
  Journal                  = {Biochimica et biophysica acta},
  Year                     = {2014},
  Month                    = {Sep},
  Number                   = {5},
  Pages                    = {1041–1058},
  Volume                   = {1850},
  Doi                      = {10.1016/j.bbagen.2014.09.007},
  ISSN                     = {0006-3002},
}

@Article{Goetz2012,
  Title                    = {Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.},
  Author                   = {Götz, Andreas W and Williamson, Mark J and Xu, Dong and Poole, Duncan and Le Grand, Scott and Walker, R. C.},
  Journal                  = {Journal of chemical theory and computation},
  Year                     = {2012},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {1542–1555},
  Volume                   = {8},

  Abstractnote             = {We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. We recommend the use of the mixed-precision SPDP model since the numerical results obtained are comparable with those of the full double precision DPDP model and the reference double precision CPU implementation but at significantly reduced computational cost. Our implementation provides performance for GB simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers.},
  Doi                      = {10.1021/ct200909j},
  ISSN                     = {1549-9618},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/ct200909j}
}

@Article{Izadi2014,
  Title                    = {Building Water Models: A Different Approach.},
  Author                   = {Izadi, Saeed and Anandakrishnan, Ramu and Onufriev, Alexey V},
  Journal                  = {The journal of physical chemistry letters},
  Year                     = {2014},

  Month                    = {Nov},
  Number                   = {21},
  Pages                    = {3863–3871},
  Volume                   = {5},

  Doi                      = {10.1021/jz501780a},
  ISSN                     = {1948-7185},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/jz501780a}
}

@Article{Jorgensen1983,
  Title                    = {Comparison of simple potential functions for simulating liquid water},
  Author                   = {Jorgensen, W. L. and Chandrasekhar, J. and Madura, J. D. and Impey, R. W. and Klein, M. L.},
  Journal                  = {Journal of Chemical Physics},
  Year                     = {1983},
  Number                   = {2},
  Pages                    = {926},
  Volume                   = {79},

  Doi                      = {10.1063/1.445869},
  ISSN                     = {00219606},
  Url                      = {http://link.aip.org/link/JCPSA6/v79/i2/p926/s1/html}
}

@Article{Joung2008,
  Title                    = {Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations},
  Author                   = {Joung, In Suk and Cheatham 3rd, Thomas. E.},
  Journal                  = {The Journal of Physical Chemistry B},
  Year                     = {2008},
  Pages                    = {9020–9041},
  Volume                   = {112},

  Doi                      = {10.1021/jp8001614}
}

@Article{Joung2008a,
  Title                    = {Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.},
  Author                   = {Joung, In Suk and Cheatham 3rd, Thomas. E.},
  Journal                  = {The Journal of Physical Chemistry B},
  Year                     = {2008},
  Number                   = {40},
  Pages                    = {13279–13290},
  Volume                   = {113},

  Doi                      = {10.1021/jp902584c}
}

@Article{Kulkarni2017,
  Title                    = {Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition},
  Author                   = {Kulkarni, Mandar and Mukherjee, Arnab},
  Journal                  = {Progress in Biophysics and Molecular Biology},
  Year                     = {2017},
  Month                    = {Sep},
  Pages                    = {63–73},
  Volume                   = {128},
  Publisher                = {Pergamon},
    Doi                      = {10.1016/j.pbiomolbio.2017.05.009}
}

@Article{Langridge1960,
  Title                    = {The molecular configuration of deoxyribonucleic acid:: I. X-ray diffraction study of a crystalline form of the lithium salt},
  Author                   = {Langridge, R. and Wilson, H. R. and Hooper, C. W.},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {1960},
  Number                   = {1},
  Pages                    = {19–37},
  Volume                   = {2},

  Doi                      = {10.1016/S0022-2836(60)80004-6},
  ISSN                     = {0022-2836},
  Publisher                = {Academic Press Inc. (London) Ltd.},
}

@Article{Lavery2014,
  Title                    = {Analyzing ion distributions around DNA},
  Author                   = {Lavery, Richard and Maddocks, John H. and Pasi, Marco and Zakrzewska, Krystyna},
  Journal                  = {Nucleic Acids Research},
  Year                     = {2014},

  Month                    = {Jul},
  Number                   = {12},
  Pages                    = {8138–8149},
  Volume                   = {42},

  Abstractnote             = {We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.},
  Doi                      = {10.1093/nar/gku504},
  ISSN                     = {0305-1048},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/24906882}
}

@Article{Lavery2009,
  Title                    = {Conformational analysis of nucleic acids revisited: Curves+.},
  Author                   = {Lavery, R. and Moakher, M. and Maddocks, J. H. and Petkeviciute, D. and Zakrzewska, K.},
  Journal                  = {Nucleic Acids Research},
  Year                     = {2009},

  Month                    = {Sep},
  Number                   = {17},
  Pages                    = {5917–5929},
  Volume                   = {37},

  Abstractnote             = {We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.},
  Doi                      = {10.1093/nar/gkp608},
  ISSN                     = {1362-4962},
  Url                      = {http://nar.oxfordjournals.org/content/37/17/5917.abstract}
}

@Article{Li2017,
  Title                    = {Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.},
  Author                   = {Li, Hui and Chowdhary, Janamejaya and Huang, Lei and He, Xibing and MacKerell, Alexander D and Roux, Benoît and Roux, Benoît},
  Journal                  = {Journal of chemical theory and computation},
  Year                     = {2017},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {4535–4552},
  Volume                   = {13},

  Abstractnote             = {Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations. Building on the first-generation Drude polarizable force field for the dipalmitoylphosphatidylcholine 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecule, the present effort was undertaken to improve this initial model and expand the force field to a wider range of phospholipid molecules. New lipids parametrized include dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), dipalmitoylphosphatidylethanolamine (DPPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers. A parametrization strategy based on a restrained ensemble-maximum entropy methodology was used to help accurately match the experimental NMR order parameters in the polar headgroup region. All the parameters were developed to be compatible with the remainder of the Drude polarizable force field, which includes water, ions, proteins, DNA, and selected carbohydrates.},
  Doi                      = {10.1021/acs.jctc.7b00262},
  ISSN                     = {1549-9626},
  Publisher                = {NIH Public Access},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/28731702}
}

@Article{Marvin1961,
  Title                    = {The molecular configuration of deoxyribonucleic acid III. X-ray diffraction study of the C form of the lithium salt},
  Author                   = {Marvin, D.A. and Spencer, M. and Wilkins, M.H.F. and Hamilton, L.D.},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {1961},

  Month                    = {Oct},
  Number                   = {5},
  Pages                    = {547-IN14},
  Volume                   = {3},

  Abstractnote             = {The lithium salt of deoxyribonucleic acid may have either of two distinct molecular configurations, B or C. The B and C X-ray diffraction patterns are very similar, but these are nevertheless distinct. The distinction is accounted for by slight differences between the configurations. Depending on conditions in the fibres, molecules in the C form may pack in either a hexagonal or anorthorhombiclattice; these conditions (e.g. water content and salt content) are discussed. Techniques used in analysing partly-disordered diffraction patterns are described. The C configuration consists of a non-integral helix with about 9⅓ residues in a pitch of 31Å; the base pairs are moved from their positions in the B model by 1·5 Å in such a direction that the narrow groove is made deeper, and are tilted by 6°. The configuration of a single nucleotide is essentially the same as in B: only the position and orientation of the nucleotides within the helix have been altered. Packing of smooth double helices in orthorhombic and hexagonal lattices is discussed, and the conclusions are applied to the packing of C molecules.},
  Doi                      = {10.1016/S0022-2836(61)80021-1},
  ISSN                     = {0022-2836},
  Publisher                = {Academic Press},
}

@Article{McFail-Isom1999,
  Title                    = {DNA structure: cations in charge?},
  Author                   = {McFail-Isom, Lori and Sines, Chad C and Williams, Loren Dean},
  Journal                  = {Current Opinion in Structural Biology},
  Year                     = {1999},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {298–304},
  Volume                   = {9},

  Abstractnote             = {Recent X-ray diffraction, NMR spectroscopy and molecular mechanics results suggest that monovalent cations selectively partition into the minor groove of AT-tracts in DNA. These observations are consistent with DNA deformation by electrostatic collapse around areas of uneven cation density. This model predicts the occurrence of known DNA deformations, such as AT-tract bending and changes in the minor-groove width.},
  Doi                      = {10.1016/S0959-440X(99)80040-2},
  ISSN                     = {0959-440X},
  Publisher                = {Elsevier Current Trends},
  Url                      = {https://www.sciencedirect.com/science/article/pii/S0959440X99800402}
}

@Article{modesto09,
  Title                    = {The impact of monovalent ion force field model in nucleic acids simulations.},
  Author                   = {Noy, Agnes and Soteras, Ignacio and Luque, F Javier and Orozco, Modesto},
  Journal                  = {Physical chemistry chemical physics},
  Year                     = {2009},
  Month                    = {Dec},
  Number                   = {45},
  Pages                    = {10596–607},
  Volume                   = {11},
  Doi                      = {10.1039/b912067j},
  ISSN                     = {1463-9084},
  Publisher                = {The Royal Society of Chemistry},
  Url                      = {http://pubs.rsc.org/en/content/articlehtml/2009/cp/b912067j}
}

@Article{Pastor1988,
  Title                    = {An analysis of the accuracy of Langevin and molecular dynamics algorithms},
  Author                   = {Pastor, R. W. and Brooks, B. R. and Szabo, A.},
  Journal                  = {Molecular Physics},
  Year                     = {1988},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {1409–1419},
  Volume                   = {65},

  Abstractnote             = {Analytic expressions for mean squared positions and velocities of a harmonic oscillator are derived for Langevin dynamics algorithms valid in the high and low friction limits, and for the Verlet algorithm. For typical values of the parameters, errors in the positions are small. However, if the velocity is defined by the usual Verlet form, kinetic energies (and therefore calculated temperatures) can be in error by several per cent for the Langevin algorithms. If the Bunger-Brooks-Karplus algorithm is used to calculate positions, a simple redefinition of the velocity results greatly in improved kinetic energies. In addition, due to cancellation of errors in the velocities and the positions, the correct virial is obtained. The effect of including the force derivative in diffusive algorithms is examined. Positional and velocity averages are calculated for the Verlet algorithm for arbitrary initial conditions, and errors in the total energy and virial are analysed. Connection is made with the Langevin algorithms, and it is shown for harmonic oscillators that different definitions of the velocity are required to optimally calculate the temperature, pressure, and total energy, respectively. Analytic expressions for mean squared positions and velocities of a harmonic oscillator are derived for Langevin dynamics algorithms valid in the high and low friction limits, and for the Verlet algorithm. For typical values of the parameters, errors in the positions are small. However, if the velocity is defined by the usual Verlet form, kinetic energies (and therefore calculated temperatures) can be in error by several per cent for the Langevin algorithms. If the Bunger-Brooks-Karplus algorithm is used to calculate positions, a simple redefinition of the velocity results greatly in improved kinetic energies. In addition, due to cancellation of errors in the velocities and the positions, the correct virial is obtained. The effect of including the force derivative in diffusive algorithms is examined. Positional and velocity averages are calculated for the Verlet algorithm for arbitrary initial conditions, and errors in the total energy and virial are analysed. Connection is made with the Langevin algorithms, and it is shown for harmonic oscillators that different definitions of the velocity are required to optimally calculate the temperature, pressure, and total energy, respectively.},
  Doi                      = {10.1080/00268978800101881},
  ISSN                     = {0026-8976},
  Publisher                = {Taylor \& Francis},
  Url                      = {http://www.tandfonline.com/doi/abs/10.1080/00268978800101881}
}

@Article{Perez2007,
  Title                    = {Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.},
  Author                   = {Pérez, A. and Marchán, I. and Svozil, D. and Šponer, J. and Cheatham 3rd, Thomas. E. and Laughton, C. A. and Orozco, M.},
  Journal                  = {Biophysical Journal},
  Year                     = {2007},

  Month                    = {Jun},
  Number                   = {11},
  Pages                    = {3817–3829},
  Volume                   = {92},

  Abstractnote             = {We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution.},
  Doi                      = {10.1529/biophysj.106.097782},
  ISSN                     = {0006-3495},
  Url                      = {http://www.cell.com/biophysj/fulltext/S0006-3495(07)71182-7}
}

@Article{Roe2018,
  Title                    = {Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data},
  Author                   = {Roe, Daniel R. and Cheatham 3rd, Thomas E.},
  Journal                  = {Journal of Computational Chemistry},
  Year                     = {2018},

  Month                    = oct,
  Doi                      = {10.1002/jcc.25382},
  ISSN                     = {01928651},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/30368859}
}

@Article{Roe2013,
  Title                    = {PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data},
  Author                   = {Roe, Daniel R. and Cheatham 3rd, Thomas E.},
  Journal                  = {Journal of Chemical Theory and Computation},
  Year                     = {2013},

  Month                    = {Jun},
  Number                   = {7},
  Pages                    = {3084–3095},
  Volume                   = {9},

  Abstractnote             = {We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ. We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ.},
  Doi                      = {10.1021/ct400341p},
  ISSN                     = {1549-9618},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/ct400341p}
}

@Article{Rueda2004,
  Title                    = {Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?},
  Author                   = {Rueda, Manuel and Cubero, Elena and Laughton, Charles A and Orozco, Modesto},
  Journal                  = {Biophysical journal},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {2},
  Pages                    = {800–11},
  Volume                   = {87},

  Abstractnote             = {The counterion distribution around a DNA dodecamer (5’-CGCGAATTCGCG-3’) is analyzed using both standard and novel techniques based on state of the art molecular dynamics simulations. Specifically, we have explored the population of Na(+) in the minor groove of DNA duplex, and whether or not a string of Na(+) can replace the spine of hydration in the narrow AATT minor groove. The results suggest that the insertion of Na(+) in the minor groove is a very rare event, but that when once the ion finds specific sites deep inside the groove it can reside there for very long periods of time. According to our simulation the presence of Na(+) inside the groove does not have a dramatic influence in the structure or dynamics of the duplex DNA. The ability of current MD simulations to obtain equilibrated pictures of the counterion atmosphere around DNA is critically discussed.},
  Doi                      = {10.1529/biophysj.104.040451},
  ISSN                     = {0006-3495},
  Publisher                = {The Biophysical Society},
  Url                      = {http://www.ncbi.nlm.nih.gov/pubmed/15298889}
}

@Book{Saenger1988,
  Title                    = {Principles of Nucleic Acid Structure.},
  Author                   = {Saenger, W.},
  Publisher                = {Springer-Verlag},
  Year                     = {1988},
  Month                    = {Aug},

  Place                    = {New York, New York, USA}
}

@Article{Saenger1986,
  Title                    = {DNA conformation is determined by economics in the hydration of phosphate groups},
  Author                   = {Saenger, Wolfram and Hunter, William N. and Kennard, Olga},
  Journal                  = {Nature},
  Year                     = {1986},

  Month                    = {Nov},
  Number                   = {6095},
  Pages                    = {385–388},
  Volume                   = {324},

  Abstractnote             = {DNA conformation is determined by economics in the hydration of phosphate groups},
  Doi                      = {10.1038/324385a0},
  ISSN                     = {0028-0836},
  Publisher                = {Nature Publishing Group},
  Url                      = {http://www.nature.com/articles/324385a0}
}

@Article{Salomon-Ferrer2013,
  Title                    = {Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald},
  Author                   = {Salomon-Ferrer, Romelia and G{\"{o}}tz, Andreas W. and Poole, Duncan and Grand, Scott Le and Walker, R. C. and Le Grand, Scott and Walker, R. C.},
  Journal                  = {Journal of Chemical Theory and Computation},
  Year                     = {2013},

  Month                    = sep,
  Number                   = {9},
  Pages                    = {3878–3888},
  Volume                   = {9},
  Doi                      = {10.1021/ct400314y},
  ISSN                     = {1549-9618},
  Publisher                = {American Chemical Society}
}

@Article{Sharp1995,
  Title                    = {Salt effects on nucleic acids.},
  Author                   = {Sharp, K A and Honig, B},
  Journal                  = {Current opinion in structural biology},
  Year                     = {1995},
  Number                   = {3},
  Pages                    = {323–8},
  Volume                   = {5},
  Doi                      = {10.1016/0959-440X(95)80093-X}
}

@Article{Smith1994,
  Title                    = {Computer simulations of NaCl association in polarizable water},
  Author                   = {Smith, D. E. and Dang, L. X.},
  Journal                  = {The Journal of Chemical Physics},
  Year                     = {1994},

  Month                    = {Mar},
  Number                   = {5},
  Pages                    = {3757},
  Volume                   = {100},

  Doi                      = {10.1063/1.466363},
  ISSN                     = {00219606},
  Url                      = {http://link.aip.org/link/?JCPSA6/100/3757/1}
}

@Article{Song2006,
  Title                    = {The effect of salt concentration on DNA conformation transition: a molecular-dynamics study},
  Author                   = {Song, Chen and Xia, Yueyuan and Zhao, Mingwen and Liu, Xiangdong and Li, Feng and Ji, Yanju and Huang, Boda and Yin, Yanyan},
  Journal                  = {Journal of Molecular Modeling},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {249–254},
  Volume                   = {12},

  Doi                      = {10.1007/s00894-005-0023-9},
  ISSN                     = {1610-2940},
  Publisher                = {Springer-Verlag},
  Url                      = {http://link.springer.com/10.1007/s00894-005-0023-9}
}

@Article{Waters2016,
  Title                    = {Transitions of Double-Stranded DNA Between the A- and B-Forms},
  Author                   = {Waters, James T. and Lu, Xiang-Jun and Galindo-Murillo, Rodrigo and Gumbart, James C. and Kim, Harold D. and Cheatham, Thomas E. and Harvey, Stephen C.},
  Journal                  = {The Journal of Physical Chemistry B},
  Year                     = {2016},

  Month                    = {Aug},
  Number                   = {33},
  Pages                    = {8449–8456},
  Volume                   = {120},

  Abstractnote             = {The structure of double-stranded DNA (dsDNA) is sensitive to solvent conditions. In solution, B-DNA is the favored conformation under physiological conditions, while A-DNA is the form found under low water activity. The A-form is induced locally in some protein–DNA complexes, and repeated transitions between the B- and A-forms have been proposed to generate the forces used to drive dsDNA into viral capsids during genome packaging. Here, we report analyses on previous molecular dynamics (MD) simulations on B-DNA, along with new MD simulations on the transition from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI), a new metric along the A-B continuum, to quantify our results. When A-DNA is placed in an equilibrated solution at physiological ionic strength, there is no energy barrier to the transition to the B-form, which begins within about 1 ns. The transition is essentially complete within 5 ns, although occasionally a stretch of a few base pairs will remain A-like for up to ∼10 ns. A compari...},
  Doi                      = {10.1021/acs.jpcb.6b02155},
  ISSN                     = {1520-6106},
  Publisher                = {American Chemical Society},
  Url                      = {http://pubs.acs.org/doi/10.1021/acs.jpcb.6b02155}
}

@Article{Weiner1986,
  Title                    = {An all atom force field for simulations of proteins and nucleic acids},
  Author                   = {Weiner, Scott J. and Kollman, Peter A. and Nguyen, Dzung T. and Case, David A.},
  Journal                  = {Journal of Computational Chemistry},
  Year                     = {1986},

  Month                    = {Apr},
  Number                   = {2},
  Pages                    = {230–252},
  Volume                   = {7},

  Doi                      = {10.1002/jcc.540070216},
  ISSN                     = {0192-8651},
  Url                      = {http://doi.wiley.com/10.1002/jcc.540070216}
}

@Article{Wu2003,
  Title                    = {Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and (31)P chemical shift anisotropy.},
  Author                   = {Wu, Z and Delaglio, F and Tjandra, N and Zhurkin, V.B and Bax, A.},
  Journal                  = {Journal of Biomolecular NMR},
  Year                     = {2003},
  Pages                    = {297–315},
  Volume                   = {26},

  Doi                      = {12815257},
  Url                      = {http://www.rcsb.org/pdb/explore.do?structureId=1NAJ}
}

@Article{Zgarbova2014,
  Title                    = {Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA},
  Author                   = {Zgarbová, Marie and Otyepka, Michal and Šponer, Jiří and Lankaš, Filip and Jurečka, Petr},
  Journal                  = {Journal of Chemical Theory and Computation},
  Year                     = {2014},

  Month                    = {Jul},
  Number                   = {8},
  Pages                    = {3177–3189},
  Volume                   = {10},

  Abstractnote             = {Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis. In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0?OL3, and ff99bsc0?OL4 force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying are consistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C?H edge/Watson?Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining part of the simulation due to geometry distortions that are transferred to several neighboring base pairs (?end effects?). We show that stability of the noncanonical structures in ff99bsc0 may be partly linked to inaccurate glycosidic (?) torsion potentials that overstabilize the syn region and allow for rapid anti to syn transitions. The RNA refined glycosidic torsion potential ?OL3 provides an improved description and substantially more stable MD simulations of RNA molecules. In the case of DNA, the ?OL4 correction gives only partial improvement. None of the tested force fields provide a satisfactory description of the terminal regions, indicating that further improvement is needed to achieve realistic modeling of fraying in DNA and RNA molecules.Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis. In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0?OL3, and ff99bsc0?OL4 force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying are consistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C?H edge/W…},
  Doi                      = {10.1021/ct500120v},
  ISSN                     = {1549-9618},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/ct500120v}
}

@Article{Zgarbova2015,
  Title                    = {Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.},
  Author                   = {Zgarbová, M. and Šponer, Jiří and Otyepka, Michal and Cheatham 3rd, Thomas. E. and Galindo-Murillo, R. and Jurečka, Petr},
  Journal                  = {Journal of chemical theory and computation},
  Year                     = {2015},

  Month                    = {Nov},
  Number                   = {12},
  Pages                    = {5723–5736},
  Volume                   = {11},

  Abstractnote             = {Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, βOL1, which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using βOL1 in combination with our previously introduced corrections, εζOL1 and χOL4, (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.},
  Doi                      = {10.1021/acs.jctc.5b00716},
  ISSN                     = {1549-9626},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/acs.jctc.5b00716}
}

@Article{Zichi1995,
  Title                    = {Molecular Dynamics of RNA with the OPLS Force Field. Aqueous Simulation of a Hairpin Containing a Tetranucleotide Loop},
  Author                   = {Zichi, D. A.},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {1995},

  Month                    = {Mar},
  Number                   = {11},
  Pages                    = {2957–2969},
  Volume                   = {117},

  Doi                      = {10.1021/ja00116a001},
  ISSN                     = {0002-7863},
  Publisher                = {American Chemical Society},
  Url                      = {http://dx.doi.org/10.1021/ja00116a001}
}

@Article{jenkins2017,
  Title                    = {Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes},
  Author                   = {Wedeking, J. E. and Dutta, D. and Belashov, I. A. and Jenkins, J.L.},
  Journal                  = {J. Biol. Chem.},
  Year                     = {2017},

  Month                    = {Mar},
  Number                   = {23},
  Pages                    = {9441-9450},
  Volume                   = {292},

  Doi                      = {10.1074/jbc.R117.787713},
}

@Article{bevil2016,
  Title                    = {Bridging the gap between in vitro and in vivo RNA folding},
  Author                   = {Leamy, K A and Assmann, S. M. and Mathews, D. H. and Bevilacqua P. C.},
  Journal                  = {Q. Rev. Biophys.},
  Year                     = {2016},

  Month                    = {Mar},
  Number                   = {49},
  Volume                   = {e10},
}

@Article{westhof2000,
  Title                    = {Water and ion binding around RNA and DNA (C,G) oligomers},
  Author                   = {Auffinger, P. and Westhof, E.},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {2000},
  Number                   = {5},
  Pages                    = {1113-1131},

  Doi                      = {10.1006/jmbi.2000.3894},

}

@Article{westhof2001,
  Title                    = {RNA solvation: A molecular dynamics simulation perspective},
  Author                   = {Auffinger,P. and Westhof, E.},
  Journal                  = {Biopolymers},
  Year                     = {2001},
  Number                   = {56},
  Pages                    = {266-274},

  Doi                      = {10.1002/1097-0282},

}

@Article{gb1996,
  Title                    = {Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium},
  Author                   = {Hawkins, G. D. and Cramer, C. J. and Truhlar, D. G.},
  Journal                  = {J. Phys. Chem.},
  Year                     = {1996},
  Number                   = {100},
  Pages                    = {19824-19839},

  Doi                      = {10.102/jp961710n},

}

@Article{fray09,
  Title                    = {Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N- labeled elongated DNA for the study of sequence-directed dynamics by NMR},
  Author                   = {Nikolova, E. and Hashim Al-Hashimi, M.},
  Journal                  = {Journal of Biomolecular NMR},
  Year                     = {2009},
  Number                   = {45},
  Volume                   = {1-2},
  Pages                    = {9-16},

  Doi                      = {10.1007/s10858-009-9350-y},

}

@Article{fray12,
  Title                    = {Probing sequence-specific DNA flexibility in A-Tracts and pyrimidine-purine steps by NMR},
  Author                   = {Nikolova, E. and Gavin, B. and Loan, A. and Hashim Al-Hashimi, M.},
  Journal                  = {Biochemistry},
  Year                     = {2012},
  Number                   = {51},
  Volume                   = {43},
  Pages                    = {8654-8664},

  Doi                      = {10.1021/bi3009517},
  
 }

@Article{merzions,
  Title                    = {Systematic Parameterization of Monovalent Ionss Employing the Nonbonded Model},
  Author                   = {Li, P and Song, L. F. and Merz, K. M. Jr},
  Journal                  = {J. Chem. Theory. Comput.},
  Year                     = {2015},
  Number                   = {4},
  Volume                   = {11},
  Pages                    = {1654-1657},

  Doi                      = {10.1021/ct500918t},
  
 }

@Article{mamatkulov,
  Title                    = {Force field for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties},
  Author                   = {Mamatkulov, S. and Schwierz, N.},
  Journal                  = {J. Chem. Phys.},
  Year                     = {2018},
  Number                   = {7},
  Volume                   = {148},
  Pages                    = {074505},

  Doi                      = {10.1063/1.5017694},
  
 }

@Article{liwang,
  Title                    = {Pariwise-additive force fields for selected aqueous monovalent ions from adaptive force matching},
  Author                   = {Li, J. and Wang, F.},
  Journal                  = {J. Chem. Phys.},
  Year                     = {2015},
  Number                   = {19},
  Volume                   = {143},
  Pages                    = {194505},

  Doi                      = {10.1063/1.4935599},
  
 }

@Article{jeejoongyoo,
  Title                    = {New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions},
  Author                   = {Yoo, J. and Aksimentiev, A.},
  Journal                  = {Phys. Chem Chem. Phys.},
  Year                     = {2018},
  Number                   = {20},
  Pages                    = {8432},

  Doi                      = {10.1039/c7cp08185e},
  
 }

@Article{mazurak,
  Title                    = {Titration in silico of reversible B<->A transitions in DNA},
  Author                   = {Mazur, A. K.},
  Journal                  = {J. Am. Chem. Soc.},
  Year                     = {2003},
  Number                   = {26},
  Volume                   = {125},
  Pages                    = {7849-59},

  Doi                      = {10.1021/ja034550j},
  
 }

@Article{pastor,
  Title                    = {The B- to A-DNA transition and the reorganization of solvent at the DNA surface},
  Author                   = {Pastor, N.},
  Journal                  = {Biophys. J.},
  Year                     = {2005},
  Number                   = {5},
  Volume                   = {88},
  Pages                    = {3262-75},

  Doi                      = {10.1529/biophysj.104.058339},
  
 }

@Article{feig,
  Title                    = {Sodium and Chlorine ions as part of the DNA solvation shell},
  Author                   = {Feig, B. M. and Pettit, M.},
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  Title                    = {Clustering Molecular dynamics Trajectories: 1. Characterizing the performance of Different Clustering Algorithms},
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