ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules

References

• Valleau , JP and Cohen , LK . 1980 . Primitive model electrolytes. I. Grand canonical Monte Carlo computations . J. Chem. Phys. , 72 : 5935 – 5941 .
   Web of Science ®Google Scholar
• Friedman , HL . 1960 . Mayer's ionic solution theory applied to electrolyte mixtures . J. Chem. Phys. , 32 : 1134 – 1149 .
   Web of Science ®Google Scholar
• Høye , JS and Stell , GR . 1977 . Ionic solution theory for non-ideal solvents. Potential of mean force between ions . Faraday Discuss. Chem. Soc. , 64 : 16 – 21 .
   Google Scholar
• McMillan , WG and Mayer , JE . 1945 . The statistical thermodynamics of multicomponent systems . J. Chem. Phys. , 13 : 276 – 305 .
   Web of Science ®Google Scholar
• Friedman , HL . 1977 . Introduction . Faraday Discuss. Chem. Soc. , 64 : 7 – 15 .
   Google Scholar
• McQuarrie DA 1973 Statistical mechanics Harper Collins Publishers New York, NY
   Google Scholar
• Allen MP Tildesley DJ 1987 Computer simulation of liquids Clarendon Press Oxford
   Google Scholar
• Metropolis , N , Rosenbluth , AW , Rosenbluth , MN , Teller , AE and Teller , E . 1953 . Equation of state calculations by fast computing machines . J. Chem. Phys. , 21 : 1087 – 1092 .
   Web of Science ®Google Scholar
• Norman , GE and Filinov , VS . 1969 . Investigations of phase transitions by a Monte Carlo methods . High Temp. (USSR) , 7 : 216 – 222 .
   Web of Science ®Google Scholar
• Adams , DJ . 1975 . Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid . Mol. Phys. , 29 : 307 – 311 .
   Web of Science ®Google Scholar
• Heffelfinger , GS and Lewitt , ME . 1996 . A comparison between two massively parallel algorithms for Monte Carlo computer simulation: an investigation in the grand canonical ensemble . J. Comp. Chem. , 17 : 250 – 265 .
   Web of Science ®Google Scholar
• Zara , SJ and Nicholson , D . 1990 . Grand canonical ensemble Monte Carlo simulation on a transputer array . Mol. Simul. , 5 : 245 – 261 .
   Web of Science ®Google Scholar
• Papadopoulou , A , Becker , ED , Lupkowski , M and van Swol , F . 1993 . Molecular dynamics and Monte Carlo simulations in the grand canonical ensemble: local versus global control . J. Chem. Phys. , 98 : 4897 – 4908 .
   Web of Science ®Google Scholar
• Heffelfinger , GS and van Swol , F . 1994 . Diffusion in Lennard-Jones fluids using dual control volume grand canonical molecular dynamics simulation (dcv-gcmd) . J. Chem. Phys. , 100 : 7548 – 7552 .
   Web of Science ®Google Scholar
• Im , W , Seefeld , S and Roux , B . 2000 . A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels . Biophys. J. , 79 : 788 – 801 .
   PubMed Web of Science ®Google Scholar
• Wu , GW , Lee , M and Chan , KY . 1999 . Grand canonical Monte Carlo simulation of an electrolyte with a solvent primitive model . Chem. Phys. Lett. , 307 : 419 – 424 .
   Web of Science ®Google Scholar
• Resat , H and Mezei , M . 1994 . Grand-canonical Monte-Carlo simulation of water positions in crystal hydrates . J. Am. Chem. Soc. , 116 : 7451 – 7452 .
   Web of Science ®Google Scholar
• Resat , H and Mezei , M . 1996 . Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate . Biophys. J. , 71 : 1179 – 1190 .
   PubMed Web of Science ®Google Scholar
• Hribar , B , Vlachy , V and Pizio , O . 2001 . Equilibrium properties of a model electrolyte adsorbed in quenched disordered charged media: the ROZ theory and GCMC simulations . J. Phys. Chem. B , 105 : 4727 – 4734 .
   Web of Science ®Google Scholar
• Wang , Q and Johnson , JK . 1997 . Path integral grand canonical Monte Carlo . J. Chem. Phys. , 107 : 5108 – 5117 .
   Web of Science ®Google Scholar
• Jedlovszky , P and Mezei , M . 1999 . Grand canonical ensemble Monte Carlo simulation of a lipid bilayer using extension biased rotations . J. Chem. Phys. , 111 : 10770 – 10773 .
   Web of Science ®Google Scholar
• Jayaram , B and Beveridge , DL . 1991 . Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: Excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions . J. Phys. Chem. , 95 : 2506 – 2516 .
   Web of Science ®Google Scholar
• Mills , P , Anderson , CF and Record , MT Jr. 1986 . Grand canonical Monte Carlo simulations of thermodynamic coefficients for a primitive model of DNA-salt solutions . J. Phys. Chem. , 90 : 6541 – 6548 .
   Web of Science ®Google Scholar
• Mezei , M . 1980 . A cavity-biased (T, V, μ) Monte Carlo method for the computer simulation of fluids . Mol. Phys. , 40 : 901 – 906 .
   Web of Science ®Google Scholar
• Mezei , M . 1987 . Grand-canonical ensemble Monte Carlo study of dense liquid Lennard-Jones, soft spheres and water . Mol. Phys. , 61 : 565 – 582 .
   Web of Science ®Google Scholar
• Jackson JD 1975 Classical electrodynamics 2nd Ed., John Wiley and Sons, Inc. New York, NY
   Google Scholar
• Pitzer , KS . 1984 . Ionic fluids . J. Phys. Chem. , 88 : 2689 – 2697 .
   Web of Science ®Google Scholar
• Rasaiah , JC . 1973 . A view of electrolyte solutions . J. Solution Chem. , 2 : 301 – 338 .
   Web of Science ®Google Scholar
• Friedman , HL . 1981 . Electrolyte solutions at equilibrium . Ann. Rev. Phys. Chem. , 32 : 179 – 204 .
   Web of Science ®Google Scholar
• Jayaram , B , Swaminathan , S , Beveridge , DL , Sharp , K and Honig , B . 1990 . Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the dielectric primitive model . Macromolecules , 23 : 3156 – 3165 .
   Web of Science ®Google Scholar
• Davis , ME and McCammon , JA . 1990 . Electrostatics in biomolecular structure and dynamics . Chem. Rev. , 94 : 7684 – 7692 .
   Google Scholar
• Sharp , KA and Honig , B . 1990 . Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation . J. Phys. Chem. , 94 : 7684 – 7692 .
   Web of Science ®Google Scholar
• Honig , B and Nicholls , A . 1995 . Classical electrostatics in biology and chemistry . Science , 268 : 1144 – 1149 .
   PubMed Web of Science ®Google Scholar
• R.R. Netz, H. Orland. Beyond Poisson-Boltzmann: fluctuations and correlations, 1999. arXiv:cond-mat/9902085.
   Google Scholar
• Podgornik , R and Žekš . 1988 . Inhomogneous Coulomb fluid: a functional integral approach . J. Chem. Soc. Faraday Trans. 2 , 84 : 611 – 631 .
   Google Scholar
• Nguyen , TT , Grosberg , AYu and Shklovskii , BI . 2000 . Screening of a charged particle by multivalent counterions in salty water: strong charge inversion . J. Chem. Phys. , 113 : 1110 – 1125 .
   Web of Science ®Google Scholar
• Holm C Kékicheff P Podgornik R 2001 Electrostatic Effects in Soft Matter and Biophysics NATO Science Series, Kluwer Academic Publishers Boston
   Google Scholar
• Tanaka , M and Grosberg , AY . 2001 . Giant charge inversion of a macroion due to multivalent counterions and monovalent coions: molecular dynamics sutdy . J. Chem. Phys. , 115 : 567 – 574 .
   Web of Science ®Google Scholar
• Ha , B-Y and Liu , AJ . 2001 . Effect of nonzero chain diameter on DNA condensation . Phys. Rev. E. , 63 : 021503
   Web of Science ®Google Scholar
• Coalson , RD and Duncan , A . 1992 . Systematic ionic screening theory of ions . J. Chem. Phys. , 97 : 5653 – 5661 .
   Web of Science ®Google Scholar
• Shklovskii , BI . 1999 . Screening of a macroion by multivalent ions: correlation-induced inversion of charge . Phys. Rev. E. , 60 : 5802 – 5811 .
   PubMed Web of Science ®Google Scholar
• Abbas , Z , Gunnarsson , M , Ahlberg , E and Nordholm , S . 2002 . Corrected Debye-Hückel theory of salt solutions: size asymmetry and effective diameters . J. Phys. Chem. B. , 106 : 1403 – 1420 .
   Web of Science ®Google Scholar
• Brush , SG , Sahlin , HL and Teller , E . 1966 . Monte Carlo study of a one-component plasma. i . J. Chem. Phys. , 45 : 2102 – 2118 .
   Web of Science ®Google Scholar
• Chapman , W and Quirke , N . 1985 . Metropolis Monte Carlo simulations of fluids with multiparticle moves . Physica B , 131 : 34 – 40 .
   Google Scholar
• G.S. Heffelfinger. In Proceedings of the 1992 DAGS/PC Symposium
   Google Scholar
• Valleau , JP , Cohen , LK and Card , DN . 1980 . Primitive model electrolytes. II. The symmetrical electrolyte . J. Chem. Phys. , 72 : 5942 – 5954 .
   Web of Science ®Google Scholar
• Reščič , J , Vlachy , V , Outhwaite , CW , Bhuiyan , LB and Mukherjee , AK . 1999 . A Monte-Carlo simulation and symmetric Poisson-Boltzmann study of a four-component electrolyte mixture . J. Chem. Phys. , 111 : 5514 – 5521 .
   Web of Science ®Google Scholar
• Vlachy , V , Ichiye , T and Haymet , ADJ . 1991 . Symmetric associating electrolytes: GCMC simulations and integral equation theory . J. Am. Chem. Soc. , 113 : 1077 – 1082 .
   Web of Science ®Google Scholar
• Ichiye , T and Haymet , ADJ . 1990 . Integral equation theory of ionic solutions . J. Chem. Phys. , 93 : 8954 – 8962 .
   Web of Science ®Google Scholar
• Certailler , T , Kunz , W , Turq , P and Bellissent-Funel , MC . 1990 . Lithium bromide in acetonitrile and water: a neutron scattering study . J. Phys. Condens. Matter , 3 : 9511 – 9520 .
   Web of Science ®Google Scholar
• Robinson RA Stokes RH 1959 Electrolyte solutions Butterworths Scientific Publications London
   Google Scholar
• Pitzer , KS . 1973 . Thermodynamics of electrolytes. 1. Theoretical basis and general equations . J. Phys. Chem. , 77 : 268 – 277 .
   Web of Science ®Google Scholar
• Pitzer KS 1991 Activity coefficients in electrolyte solutions 2nd Ed., CRC Press Boca Raton
   Google Scholar
• Barthel JMG Krienke H Kunz W 1998 Physical chemistry of electrolyte solutions Steinkopff/Springer Darmstadt/New York
   Google Scholar
• Allnatt AR 1964 Integral equations in ionic solution theory Mol. Phys. 8
   Google Scholar
• Rasaiah JC Friedman HL 1968 Integral equation methods in the computation of equilibrium properties of ionic solutions J. Chem. Phys. 48
   Google Scholar
• Rasaiah JC Friedman HL 1969 Integral equation computations for aqueous 1-1 electrolytes. Accuracy of the method J. Chem. Phys. 50
   Google Scholar
• Carley DD 1967 Radial distributions of ions for a primitive model of an electrolyte solution J. Chem. Phys. 46
   Google Scholar
• Rossky , PJ , Dudowicz , JB , Tembe , BL and Friedman , HL . 1980 . Ionic association in model 2-2 electrolyte solutions . J. Chem. Phys. , 73 : 3372 – 3383 .
   Web of Science ®Google Scholar
• Bacquet , R and Rossky , PJ . 1983 . Corrections to the HNC equation for associating electrolytes . J. Chem. Phys. , 79 : 1419 – 1426 .
   Web of Science ®Google Scholar
• Rasaiah JC 1972 Computations for higher valence electrolytes in the restricted primitive model J. Chem. Phys. 56
   Google Scholar
• Babu , CS and Ichiye , T . 1994 . New integral equation theory for primitive model ionic liquids: From electrolytes to molten salts . J. Chem. Phys. , 100 : 9147 – 9155 .
   Web of Science ®Google Scholar
• Cornell , WD , Cieplak , P , Bayly , CI , Gould , IR , Merz , KM Jr. , Ferguson , DM , Spellmeyer , DC , Fox , T , Caldwell , JW and Kollman , PA . 1995 . A second generation force field for the simulation of proteins, nucleic acids, and organic molecules . J. Am. Chem. Soc. , 117 : 5179 – 5197 .
   Web of Science ®Google Scholar
• Lindahl , E , Hess , B and van der Spoel , D . 2001 . GROMACS 3.0: a package for molecular simulation and trajectory analysis . J. Mol. Mod. , 7 : 306 – 317 .
   Web of Science ®Google Scholar
• Brooks , BR , Bruccoleri , RE , Olafson , BA , States , DJ , Swaminathan , A and Karplus , M . 1983 . Charmm: A program for macromolecular energy, minimization, and dynamics calculations . J. Comput. Chem. , 4 : 187 – 217 .
   Web of Science ®Google Scholar
• MacKerell AD Jr. Brooks B Brooks CL III Nilsson L Roux B Won Y Karplus M 1998 CHARMM: The energy function and its parameterization with an overview of the program The Encyclopedia of Computational Chemistry 1st Ed., John Wiley & Sons Chichester 271 277
   Google Scholar
• Sitkoff , D , Sharp , KA and Honig , B . 1994 . Accurate calculation of hydration free energies using macroscopic solvent models . J. Phys. Chem. , 98 : 1978 – 1988 .
   Web of Science ®Google Scholar
• Åqvist , J . 1990 . Ion water interaction potentials derived from free energy perturbation simulations . J. Phys. Chem. , 94 : 8021 – 8024 .
   Web of Science ®Google Scholar
• Heinzinger , K . 1985 . Computer simulations of aqueous electrolyte solutions . Physica B , 131 : 196 – 216 .
   Web of Science ®Google Scholar
• Baker , NA , Sept , D , Joseph , S , Holst , MJ and McCammon , JA . 2001 . Electrostatics of nanosystems: application to microtubules and the ribosome . Proc. Natl Acad. Sci. , 98 : 10037 – 10041 .
   PubMed Web of Science ®Google Scholar
• Matsumoto , M and Nishimura , T . 1998 . Mersenne Twister: a 623-dimensionally equidistributed uniform pseudo-random number generator . ACM Trans. Mod. Com. Sim. , 8 : 3 – 30 .
   Google Scholar
• Holst M 2001 Adaptive numerical treatment of elliptic systems on manifolds: Theory and implementation in the finite element package MC Adv. Comput. Math. Submitted
   Google Scholar
• Ramanathan , PS and Friedman , HL . 1971 . Study of a refined model for aqueous 1–1 electrolytes . J. Chem. Phys. , 54 : 1086 – 1099 .
   Web of Science ®Google Scholar
• Debye , P and Hückel , E . 1923 . Zur theorie der elektrolyte i . Phys. Z , 24 : 185 – 206 .
   Google Scholar
• Chattopadhyaya , R , Meador , WE , Means , AR and Quiocho , FA . 1992 . Calmodulin structure refined at 1.7 Å resolution . J. Mol. Biol. , 228 : 1177 – 1192 .
   PubMed Web of Science ®Google Scholar
• Babu , YS , Bugg , CE and Cook , WJ . 1988 . Structure of calmodulin refined at 2.2 Å resolution . J. Mol. Biol. , 204 : 191 – 204 .
   PubMed Web of Science ®Google Scholar
• Wilson , MA and Brunger , AT . 2000 . The 1.0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity . J. Mol. Biol. , 301 : 1237 – 1256 .
   PubMed Web of Science ®Google Scholar
• Kretsinger , RH and Nockolds , CE . 1973 . Carp muscle calcium-binding protein . J. Biol. Chem. , 248 : 3313 – 3326 .
   PubMed Web of Science ®Google Scholar
• Kretsinger RH 1975 Hypothesis: Calcium modulated proteins contain EF-hands Carafoli E Calcium transport in contraction and secretion North-Holland Publishing Amsterdam
   Google Scholar
• Nielsen , JE , Andersen , KV , Honig , B , Hooft , RW , Klebe , G , Vriend , G and Wade , RC . 1999 . Improving macromolecular electrostatics calculations . Protein Eng. , 12 : 657 – 662 .
   PubMedGoogle Scholar
• Nayal , M and DiCera , E . 1994 . Predicting Ca2+-binding sites in proteins . Proc. Natl Acad. Sci. USA , 91 : 817 – 821 .
   PubMed Web of Science ®Google Scholar
• Nayal M DiCera E 1994 Predicting Ca++-binding sites in proteins Biophys. J. 66 part 2 A62 A62
   Web of Science ®Google Scholar
• Jayaram , B and Beveridge , DL . 1996 . Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA . Annu. Rev. Biophys. Biomol. Struct. , 25 : 367 – 394 .
   PubMedGoogle Scholar
• Manning , GS . 1978 . The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides . Q. Rev. Biophys. , 2 : 179 – 246 .
   Web of Science ®Google Scholar
• Le Bret , M and Zimm , BH . 1985 . Ions about a cylindrical polyelectrolyte . Biopolymers , 23 : 271 – 285 .
   Google Scholar
• Gordon , H and Goldman , S . 1992 . Simulations on the counterion and solvent distribution functions around two simple models of a polyelectrolyte . J. Phys. Chem. , 96 : 1921 – 1932 .
   Web of Science ®Google Scholar
• Murthy , CS , Bacquet , RJ and Rossky , PJ . 1985 . Ionic distributions near polyelectrolytes. A comparison of theoretical approaches . J. Phys. Chem. , 89 : 701 – 710 .
   Web of Science ®Google Scholar
• Mills , P , Anderson , CF and Record , MT Jr. 1985 . Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories . J. Phys. Chem. , 89 : 3984 – 3994 .
   Web of Science ®Google Scholar
• Young , MA , Jayaram , B and Beveridge , DL . 1997 . Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets . J. Am. Chem. Soc. , 119 : 59 – 69 .
   Web of Science ®Google Scholar
• Feig , M and Pettitt , BM . 1999 . Sodium and chlorine ions as part of the DNA solvation shell . Biophys. J. , 77 : 1769 – 1781 .
   PubMed Web of Science ®Google Scholar
• Kielkopf , CL , Ding , S , Kuhn , P and Rees , C . 2000 . Conformational flexibility of B-DNA at 0.74 Å resolution: d(CCAGTACTGG)2 . J. Mol. Biol. , 296 : 787 – 801 .
   PubMed Web of Science ®Google Scholar