142
Views
8
CrossRef citations to date
0
Altmetric
Proceedings of the 3rd International Conference on Molecular Simulation

Application of isotropic periodic sum method for 4-pentyl-4′-cyanobiphenyl liquid crystal

, , , &
Pages 927-935 | Received 31 Jan 2014, Accepted 01 Dec 2014, Published online: 22 Jan 2015

References

  • Ewald P. The calculation of optical and electrostatic grid potential. Ann Phys. 1921;64:253–287.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
  • Essmann U, Perera L, Berkowitz M, Darden T, Lee H, Pedersen L. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.
  • Kia A, Kim D, Darve E. Fast electrostatic force calculation on parallel computer clusters. J Comput Phys. 2008;227:8551–8567.
  • Yokota R, Barba LA, Narumi T, Yasuoka K. Petascale turbulence simulation using a highly parallel fast multipole method on GPUs. Comput Phys Commun. 2013;184:445–455.
  • Roberts J, Schnitker J. How the unit cell surface charge distribution affects the energetics of ion–solvent interactions in simulations. J Chem Phys. 1994;101:5024–5031.
  • Roberts J, Schnitker J. Boundary conditions in simulations of aqueous ionic solutions: a systematic study. J Phys Chem. 1995;99:1322–1331.
  • Luty B, Van Gunsteren W. Calculating electrostatic interactions using the particle–particle particle–mesh method with nonperiodic long-range interactions. J Phys Chem. 1996;100:2581–2587.
  • Hünenberger PH, McCammon JA. Ewald artifacts in computer simulations of ionic solvation and ion–ion interaction: a continuum electrostatics study. J Chem Phys. 1999;110:1856–1872.
  • Hünenberger P, McCammon J. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem. 1999;78:69–88.
  • Weber W, Hünenberger P, McCammon J. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B. 2000;104:3668–3675.
  • Patra M, Karttunen M, Hyvönen M, Falck E, Lindqvist P, Vattulainen I. Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J. 2003;84:3636–3645.
  • Patra M, Karttunen M, Hyvönen M, Falck E, Vattulainen I. Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions. J Phys Chem B. 2004;108:4485–4494.
  • Monticelli L, Simões C, Belvisi L, Colombo G. Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides. J Phys: Condens Matter. 2006;18:S329–S345.
  • Hoheisel C. Bulk viscosity of model fluids. A comparison of equilibrium and nonequilibrium molecular dynamics results. J Chem Phys. 1987;86:2328–2333.
  • Hoheisel C, Vogelsang R, Schoen M. Bulk viscosity of the Lennard-Jones fluid for a wide range of states computed by equilibrium molecular dynamics. J Chem Phys. 1987;87:7195–7198.
  • Smit B. Phase diagrams of Lennard-Jones fluids. J Chem Phys. 1992;96:8639–8640.
  • Trokhymchuk A, Alejandre J. Computer simulations of liquid/vapor interface in Lennard-Jones fluids: some questions and answers. J Chem Phys. 1999;111:8510–8523.
  • Lopez-Lemus J, Alejandre J. Thermodynamic and transport properties of simple fluids using lattice sums: bulk phases and liquid–vapour interface. Mol Phys. 2002;100:2983–2992.
  • Neumann M, Steinhauser O. The influence of boundary conditions used in machine simulations on the structure of polar systems. Mol Phys. 1980;39:437–454.
  • Alper HE, Levy RM. Computer simulations of the dielectric properties of water: studies of the simple point charge and transferrable intermolecular potential models. J Chem Phys. 1989;91:1242–1251.
  • Kitchen D, Hirata F, Westbrook J, Levy R, Kofke D, Yarmush M. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water. J Comput Chem. 1990;11:1169–1180.
  • Tasaki K, McDonald S, Brady J. Observations concerning the treatment of long-range interactions in molecular dynamics simulations. J Comput Chem. 1993;14:278–284.
  • Smith PE, Gunsterenvan WF. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J Chem Phys. 1994;100:3169–3174.
  • Feller S, Pastor R, Rojnuckarin A, Bogusz S, Brooks B. Effect of electrostatic force truncation on interfacial and transport properties of water. J Phys Chem. 1996;100:17011–17020.
  • vander Spoel D, Maarenvan PJ, Berendsen HJ. A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field. J Chem Phys. 1998;108:10220–10230.
  • Mark P, Nilsson L. Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comput Chem. 2002;23:1211–1219.
  • Yonetani Y. A severe artifact in simulation of liquid water using a long cut-off length: appearance of a strange layer structure. Chem Phys Lett. 2005;406:49–53.
  • van der Spoel D, Maarenvan P. The origin of layer structure artifacts in simulations of liquid water. J Chem Theor Comput. 2006;2:1–11.
  • Yonetani Y. Liquid water simulation: a critical examination of cutoff length. J Chem Phys. 2006;124:204501.
  • Takahashi KZ. Truncation effects of shift function methods in bulk water systems. Entropy. 2013;15:3249–3264.
  • Loncharich R, Brooks B. The effects of truncating long-range forces on protein dynamics. Proteins Struct Funct Bioinf. 1989;6:32–45.
  • Schreiber H, Steinhauser O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry. 1992;31:5856–5860.
  • Schreiber H, Steinhauser O. Molecular dynamics studies of solvated polypeptides: why the cut-off scheme does not work. Chem Phys. 1992;168:75–89.
  • Schreiber H, Steinhauser O. Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides: the reaction field method. Journal of molecular biology. 1992;228:909–923.
  • Saito M. Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions. Mol Simul. 1992;8:321–333.
  • Guenot J, Kollman P. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J Comput Chem. 1993;14:295–311.
  • Saito M. Molecular dynamics simulations of proteins in solution: artifacts caused by the cutoff approximation. J Chem Phys. 1994;101:4055–4061.
  • Oda K, Miyagawa H, Kitamura K. How does the electrostatic force cut-off generate non-uniform temperature distributions in proteins? Mol Simul. 1996;16:167–177.
  • Norberg J, Nilsson L. On the truncation of long-range electrostatic interactions in DNA. Biophys J. 2000;79:1537–1553.
  • Beck D, Armen R, Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry. 2005;44:609–616.
  • Reif M, Kräutler V, Kastenholz M, Daura X, Hünenberger P. Molecular dynamics simulations of a reversibly folding β-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. J Phys Chem B. 2009;113:3112–3128.
  • Mazars M. Long ranged interactions in computer simulations and for quasi-2D systems. Phys Rep. 2011;500:43–116.
  • Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS One. 2012;7(e39918)
  • Wu X, Brooks B. Isotropic periodic sum: a method for the calculation of long-range interactions. J Chem Phys. 2005;122:044107.
  • Wu X, Brooks B. Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems. J Chem Phys. 2008;129:154115.
  • Wu X, Brooks B. Isotropic periodic sum of electrostatic interactions for polar systems. J Chem Phys. 2009;131:024107.
  • Ojeda-May P, Pu J. Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation. J Chem Phys. 2014;140:164106.
  • Takahashi K, Yasuoka K, Narumi T. Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid. J Chem Phys. 2007;127:114511.
  • Takahashi K, Narumi T, Yasuoka K. Cutoff radius effect of the isotropic periodic sum method in homogeneous system. II. Water. J Chem Phys. 2010;133:014109.
  • Takahashi K, Narumi T, Yasuoka K. Cut-off radius effect of the isotropic periodic sum method for polar molecules in a bulk water system. Mol Simul. 2012;38:397–403.
  • Nakamura H, Ohto T, Nagata Y. Polarizable site charge model at liquid/solid interfaces for describing surface polarity: application to structure and molecular dynamics of water/rutile TiO2 (110) interface. J Chem Theor Comput. 2013;9:1193–1201.
  • Ohto T, Mishra A, Yoshimune S, Nakamura H, Bonn M, Nagata Y. Influence of surface polarity on water dynamics at the water/rutile TiO2 (110) interface. J Phys Condens Matter. 2014;26:244102.
  • Klauda J, Wu X, Pastor R, Brooks B. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. J Phys Chem B. 2007;111:4393–4400.
  • Takahashi KZ, Narumi T, Yasuoka K. Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid–vapor interfaces of water. J Chem Phys. 2011;134:174112.
  • Venable R, Chen L, Pastor R. Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers. J Phys Chem B. 2009;113:5855–5862.
  • Ojeda-May P, Pu J. Isotropic periodic sum treatment of long-range electrostatic interactions in combined quantum mechanical and molecular mechanical calculations. J Chem Theor Comput. 2014;10:134–145.
  • Takahashi KZ, Narumi T, Yasuoka K. A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics. J Chem Phys. 2011;135:174108.
  • Takahashi KZ, Narumi T, Suh D, Yasuoka K. An improved isotropic periodic sum method using linear combinations of basis potentials. J Chem Theor Comput. 2012;8:4503–4516.
  • Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev. 2014;114:779–814.
  • Takahashi KZ. Design of a reaction field using a linear-combination-based isotropic periodic sum method. J Comput Chem. 2014;35:865–875.
  • Takahashi KZ, Yasuoka K. Application of a linear-combination-based isotropic periodic sum method for ethanol liquid–vapor interface. Mol Simul. 2014 (in press) :1–6.
  • Takahashi KZ. An improvement of truncation method by a novel reaction field: accurate computation for estimating methanol liquid–vapor interfacial systems. Comput Mater Sci. in press.
  • Takahashi KZ. Application of a novel reaction field for coarse-grained molecular dynamics simulations of zwitterionic lipid systems. Comput Mater Sci. Submitted for publication.
  • Gay J, Berne B. Modification of the overlap potential to mimic a linear site–site potential. J Chem Phys. 1981;74:3316–3319.
  • Kremer K, Grest GS. Dynamics of entangled linear polymer melts: a molecular-dynamics simulation. J Chem Phys. 1990;92:5057.
  • Barberi R, Durand G. Order parameter of a nematic liquid crystal on a rough surface. Phys Rev A. 1990;41:2207–2210.
  • Guo W, Fung B. Determination of the order parameters of liquid crystals from carbon-13 chemical shifts. J Chem Phys. 1991;95:3917–3923.
  • Cramer C, Cramer T, Kremer F, Stannarius R. Measurement of orientational order and mobility of a nematic liquid crystal in random nanometer confinement. J Chem Phys. 1997;106:3730–3742.
  • Ossowska-Chruściel M, Korlacki R, Kocot A, Wrzalik R, Chruściel J, Zalewski S. Infrared study of orientational order parameters of a ferroelectric liquid crystal. Phys Rev E. 2004;70:041705.
  • Sanchez-Castillo A, Osipov MA, Giesselmann F. Orientational order parameters in liquid crystals: a comparative study of X-ray diffraction and polarized Raman spectroscopy results. Phys Rev E. 2010;81:021707.
  • Cross C, Fung B. A simplified approach to molecular dynamics simulations of liquid crystals with atom–atom potentials. J Chem Phys. 1994;101:6839–6848.
  • Komolkin AV, Laaksonen A, Maliniak A. Molecular dynamics simulation of a nematic liquid crystal. J Chem Phys. 1994;101:4103–4116.
  • Wang Z, Lupo JA, Patnaik S, Pachter R. Large scale molecular dynamics simulations of a 4-n-pentyl-4-cyanobiphenyl (5CB) liquid crystalline model in the bulk and as a droplet. Comput Theor Polym Sci. 2001;11:375–387.
  • Stevensson B, Komolkin AV, Sandström D, Maliniak A. Structure and molecular ordering extracted from residual dipolar couplings: a molecular dynamics simulation study. J Chem Phys. 2001;114:2332–2339.
  • Cacelli I, Campanile S, Prampolini G, Tani A. Stability of the nematic phase of 4-n-pentyl-4-cyanobiphenyl studied by computer simulation using a hybrid model. J Chem Phys. 2002;117:448–453.
  • Amovilli C, Cacelli I, Campanile S, Prampolini G. Calculation of the intermolecular energy of large molecules by a fragmentation scheme: application to the 4-n-pentyl-4-cyanobiphenyl (5CB) dimer. J Chem Phys. 2002;117:3003–3012.
  • Cacelli I, Prampolini G, Tani A. Atomistic simulation of a nematogen using a force field derived from quantum chemical calculations. J Phys Chem B. 2005;109:3531–3538.
  • McDonald AJ, Hanna S. Atomistic simulation of a model liquid crystal. J Chem Phys. 2006;124:164906.
  • Cacelli I, De Gaetani L, Prampolini G, Tani A. Liquid crystal properties of the n-alkyl-cyanobiphenyl series from atomistic simulations with ab initio derived force fields. J Phys Chem B. 2007;111:2130–2137.
  • Tiberio G, Muccioli L, Berardi R, Zannoni C. Towards in silico liquid crystals. realistic transition temperatures and physical properties for n-cyanobiphenyls via molecular dynamics simulations. ChemPhysChem. 2008;10:125–136.
  • Cifelli M, De Gaetani L, Prampolini G, Tani A. Atomistic computer simulation and experimental study on the dynamics of the n-cyanobiphenyls mesogenic series. J Phys Chem B. 2008;112:9777–9786.
  • De Gaetani L, Prampolini G. Computational study through atomistic potentials of a partial bilayer liquid crystal: structure and dynamics. Soft Matter. 2009;5:3517–3526.
  • Zhang J, Su J, Guo H. An atomistic simulation for 4-cyano-4-pentylbiphenyl and its homologue with a reoptimized force field. J Phys Chem B. 2011;115:2214–2227.
  • Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc. 1984;106:765–784.
  • Jorgensen WL, Madura JD, Swenson CJ. Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc. 1984;106:6638–6646.
  • Jorgensen WL, Laird ER, Nguyen TB, Tirado-Rives J. Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions. J Comput Chem. 1993;14:206–215.
  • Jorgensen WL, Nguyen TB. Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions. J Comput Chem. 2004;14:195–205.
  • Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys. 1980;72:2384–2393.
  • Nosé S. A molecular dynamics method for simulations in the canonical ensemble. Mol Phys. 1984;52:255–268.
  • Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys. 1984;81:511–519.
  • Swope WC, Andersen HC, Berens PH, Wilson KR. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J Chem Phys. 1982;76:637–649.
  • Andersen H. Rattle: a ‘velocity’ version of the shake algorithm for molecular dynamics calculations. J Comput Phys. 1983;52:24–34.
  • Narumi T, Ohno Y, Okimoto N, Koishi T, Suenaga A, Futatsugi N, Yanai R, Himeno R, Fujikawa S, Ikei M, Taiji M. A 55 TFLOPS simulation of amyloid forming peptides from yeast prion Sup35 with the specialpurpose computer system MDGRAPE-3. Proceedings of the SC06 (high performance computing, networking, storage and analysis), CDROM; 2006 Nov. Tampa (FL): Stanford University; 2006.
  • Taiji M. MDGRAPE-3 Chip: a 165-Gflops application-specific LSI for molecular dynamics simulations. HOT CHIPS 16; 2004 Aug. Stanford University; 2004.
  • Taiji M, Narumi T, Ohno Y, Futatsugi N, Suenaga A, Takada N, Konagaya A. A petaflops special-purpose computer system for molecular dynamics simulations. Proceedings of the SC2003 (high performance networking and computing); 2003 Nov. Phoenix, AZ; 2003.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.