Abstract
Computer Simulations have become an important complementary technique to experiment and analytical theory for scientific discoveries. Molecular Dynamics (MD) is one of the most abundant techniques of computer modeling, and is frequently used simulation methods in biomolecular applications. Its popularity may stem from its simplicity and versatile applicability. The fundamental underlying assumption of MD is that the system consists of particles that interact via the classical equations of motion, i.e., both quantum mechanical and relativistic effects are neglected. The exclusion of these effects, however, does not generally have a significant impact on the biomolecular questions being studied.
Keywords
- Molecular Dynamic Simulation
- Lipid Bilayer
- Chem Phys
- Radial Distribution Function
- Root Mean Square Distance
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
Further Study
Allen MP, Tildesley DJ. 1987. Computer simulation of liquids. Oxford: Clarendon Press.
Frenkel D, Smit B. 1996. Understanding molecular simulation: from basic algorithms to applications. San Diego: Academic Press.
Leach A. 1997. Molecular modelling: principles and applications. Essex: Addison Wesley.
van Gunsteren WF, Billeter SR, Eising AA, Hünenberger P, Krüger AE, Mark WRP, Scott AE, Tironi IG. 1996. Biomolecular simulation: the GROMOS manual and user guide. Zürich: Vdf.
Lindahl E, Hess B, van der Spoel D. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analy-sis. J Mol Model 7(8):306-317.
Hess B, Kutzner C, van der Spoel D, Lindahl E. 2008. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4(3):435-447.
Brooks BR, Bruccoleri RE, Olafson DJ, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
MacKerel Jr AD, Brooks III CL, Nilsson L, Roux B, Won Y, Karplus M. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, Vol. 1, pp. 271-277. Ed. PvR Schleyer. Chichester: John Wiley & Sons.
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Koll-man PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic mole-cules. J Am Chem Soc 117(19):5179-5197.
References
Verlet L. 1967. Computer ‘experiments’ on classical fluids, I: thermodynamical properties of Lennard-Jonesmolecules. Phys Rev 159:98-103.
Allen MP, Tildesley DJ. 1987. Computer simulation of liquids. Oxford: Clarendon Press.
Frenkel D, Smit B. 1996. Understanding molecular simulation: from basic algorithms to applications. SanDiego: Academic Press.
Leach A. 1997. Molecular modelling: principles and applications. Essex: Addison Wesley.
Egberts E, Marrink S-J, Berendsen HJC. 1994. Molecular dynamics simulation of a phospholipid membrane.Eur Biophys J 22:423-436.
Tieleman DP, Marrink SJ, Berendsen HJC. 1997. A computer perspective of membranes: molecular dynamicsstudies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270.
Sum AK, Faller R, de Pablo JJ. 2003. Molecular simulation study of phospholipid bilayers and insights of theinteractions with disaccharides. Biophys J 85:2830-2844.
Faller R, Marrink S-J. 2004. Simulation of domain formation in mixed DLPC-DSPC lipid bilayers. Langmuir 20:7686-7693.
Lee BW, Faller R, Sum AK, Vattulainen I, Patra M, Karttunen M. 2004. Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations. Fluid Phase Equilib 225:63-68.
Switzer J, Bennun S, Longo ML, Palazoglu A, Faller R. 2006. Karhunen-Loeve analysis for pattern description in phase separated lipid bilayer systems. J Chem Phys 124:234906.
Cooke IR, Kremer K, Deserno M. 2005. Tunable generic model for fluid bilayer membranes. Phys Rev E 72:011506.
Moore PB, Lopez CF, Klein ML. 2001. Dynamical properties of a hydrated lipid bilayer from a multinanosec-ond molecular dynamics simulation. Biophys J 81:2484-2494.
Lopez CF, Nielsen SO, Moore PB, Shelley JC, Klein ML. 2002. Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations. J Phys Condens Matter 14:9431-9444.
Patra M, Karttunen M, Hyvönen MT, Falck E, Vattulainen I. 2004. Lipid bilayers driven to a wrong plane in molecular dynamics simulations by truncation of long-range electrostatic interactions. J Phys Chem B 108:4485-4494.
Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR. 1996. Effect of electrostatic force truncation on interfacial and transport properties of water. J Phys Chem 100:17011-17020.
Anezo C, de Vries AH, Holtje H, Tieleman DP, Marrink SJ. 2003. Methodological issues in lipid bilayer simu-lations. J Phys Chem B 107:9424-9433.
Farago O. 2003. "Water-free" computer model for fluid bilayer membranes. J Chem Phys 119:596-605.
Marrink SJ, de Vries AH, Mark AE. 2004. Coarse grained model for semi-quantitative lipid simulation. J PhysChem B 108:750-760.
Stevens MJ. 2004. Coarse-grained simulations of lipid bilayers. J Chem Phys 121:11942-1198.
Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Klein ML. 2001. A coarse grain model for phosphol-ipid simulations. J Phys Chem B 105:4464-4470.
Kaznessis YN, Kim ST, Larson RG. 2002. Simulations of zwitterionic and anionic phospholipid monolayers. Biophys J 82:1731-1742.
Alper HE, Bassolino D, Stouch TR. 1993. Computer simulation of a phospholipid monolayer-water system: the influence of long-range forces on water structure and dynamics. J Chem Phys 98:9798-9807.
Feller SE, Zhang YH, Pastor RW. 1995. Computer-simulation of liquid/liquid interfaces, II: surface-tension area dependence of a bilayer and a monolayer. J Chem Phys 103:10267-10276.
Heine DR, Rammohan AR, Balakrishnan J. 2007. Atomistic simulations of the interaction between lipid bilay-ers and substrates. Mol Simul 33:391-397.
Xing C, Faller R. 2008. Interactions of lipid bilayers with supports: a coarse-grained molecular simulationstudy. J Phys Chem B 112:7086-7094.
Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. 1984. Molecular dynamics with couplingto an external bath. J Chem Phys 81:3684-3690.
Essman U, Perela L, Berkowitz ML, Darden HLT, Pedersen LG. 1995. A smooth particle mesh Ewald method.J Chem Phys 103:8577-8592.
Mashl RJ, Scott HL, Subramaniam S, Jakobsson E. 2001. Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration. Biophys J 81:3005-3015.
Feller SE, Yin D, Pastor RW, MacKerel Jr. AD. 1997. Molecular dynamics simulation of unsaturated lipid bi-layers at low hydration: parameterization and comparison with diffraction studies. Biophys J 73:2269-2279.
Tieleman DP, Berendsen HJC. 1996. Molecular dynamics simulations of fully hydrated dipalmitoylphosphati-dylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys 105:4871-4880.
Balali-Mood K, Harroun TA, Bradshaw JP. 2003. Molecular dynamics simulations of a mixed DOPC/DOPGbilayer. Eur Phys J E 12:S135-S140.
Dickey A, Faller R. 2008. Examining the contributions of lipid shape and headgroup charge on bilayer behav-ior. Biophys J 95:2636-2646.
Berger O, Edholm O, Jahnig F. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphos-phatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002-2013.
Pandit SA, Bostick D, Berkowitz ML. 2003. Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics. Biophys J 85:3120-3131.
Niemela P, Hyvonen MT, Vattulainen I. 2004. Structure and dynamics of sphingomyelin bilayer: insight gained through systematic comparison to phosphatidylcholine. Biophys J 87:2976-2989.
Pandit SA, Jakobsson E, Scott HL. 2004. Simulation of the early stages of nano-domain formation in mixed bilayers of sphingomyelin, cholesterol, and dioleylphosphatidylcholine. Biophys J 87:3312-3322.
Murzyn K, Rog T, Pasienkiewicz-Gierula M. 2005. Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophys J 88:1091-1103.
Leekumjorn S, Sum AK. 2006. Molecular simulation study of structural and dynamic properties of mixedDPPC/DPPE Bilayers. Biophys J 90:3951-3965.
Gurtovenko A, Patra M, Karttunen M, Vattulainen I. 2004. Cationic DMPC/DMTAP lipid bilayers: moleculardynamics study. Biophys J 86:3461-3472.
Falck E, Patra M, Karttunen M, Hyvonen MT, Vattulainen I. 2004. Lessons of slicing membranes: interplay of packing, free area and lateral diffusion in phospholipid/cholesterol bilayers. Biophys J 87:1076-1091.
Pandit SA, Bostick D, Berkowitz ML. 2004. Complexation of phosphatidylcholine lipids with cholesterol. Bio-phys J 86:1345-1356.
Smondryev AM, Berkowitz ML. 2001. Molecular dynamics simulation of the structure of dimyristolphosphati-dylcholine bilayers with cholesterol, ergosterol and lanosterol. Biophys J 80:1649-1658.
Dickey AN, Yim W-S, Faller R. 2009. Using ergosterol to mitigate the deleterious effects of ethanol on bilayer structure. J Phys Chem B. 113:2388-2397.
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. 1997. LINCS: a linear constraint solver for molecular simu-lations. J Comput Chem 18:1463-1472.
Müller-Plathe F, Brown D. 1991. Multi-colour algorithms in molecular simulation: vectorisation and paralleli-sation of internal forces and constraints. Comput Phys Commun 64:7-14.
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. 1981. Interaction models for water in relation toprotein hydration. In Intermolecular forces, pp. 331-342. Ed. B Pullman. Dordrecht: Reidel.
Berendsen HJC, Grigera JR, Straatsma TP. 1987. The missing term in effective pair potentials. J Phys Chem 91:6269-6271.
Mackerel AD. 2004. Empirical force fields for biological macromolecules: overview and issues. J ComputChem 25:1584-1604.
Aman K, Lindahl E, Edholm O, Hakansson P, Westlund PO. 2003. Structure and dynamics of interfacial water in an L-alpha phase lipid bilayer from molecular dynamics simulations. Biophys J 84:102-115.
Pasenkiewicz-Gierula M, Takaoka Y, Miyagawa H, Kitamura K, Kusumi A. 1999. Charge pairing of headgroups in phosphatidylcholine membranes: a molecular dynamics simulation study. Biophys J 76:1228-1240.
Tieleman DP, Berendsen HJC. 1996. Molecular dynamics simulations of a fully hydrated dipalmitoyl phos-phatidylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys 105:4871-4880.
Hofsass C, Lindahl E, Edholm O. 2003. Molecular dynamics simulations of phospholipid bilayers with choles-terol. Biophys J 84:2192-2206.
Tu KC, Klein ML, Tobias DJ. 1998. Constant-pressure molecular dynamics investigation of cholesterol effectsin a dipalmitoylphosphatidylcholine bilayer. Biophys J 75:2147-2156.
Muller M, Katsov K, Schick M. 2006. Biological and synthetic membranes: what can be learned from a coarse-grained description? Phys Rep 434:113-176.
Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Moore PB, Klein ML. 2001. Simulations of phosphol-ipids using a coarse grain model. J Phys Chem B 105:9785-9792.
Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Klein ML. 2001. A coarse grain model for phosphol-ipid simulations. J Phys Chem B 105:4464-4470.
Nielsen SO, Lopez CF, Srinivas G, Klein ML. 2004. Coarse grain models and the computer simulation of softmaterials. J Phys Condens Matter 16:R481-R512.
Marrink SJ, Risselada J, Mark AE. 2005. Simulation of gel phase formation and melting in lipid bilayers usinga coarse grained model. Chem Phys Lipids 135:223-244.
Marrink SJ, Mark AE. 2004. Molecular view of hexagonal phase formation in phospholipid membranes. Bio-phys J 87:3894-3900.
Lopez CF, Moore PB, Shelley JC, Shelley MY, Klein ML. 2002. Computer simulation studies of biomem-branes using a coarse grain model. Comput Phys Commun 147:1-6.
Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. 2007. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111:7812-7824.
Bennun SV, Longo ML, Faller R. 2007. Phase and mixing behavior in two-component lipid bilayers: a molecu-lar dynamics study in DLPC/DSPC mixtures. J Phys Chem B 111:9504-9512.
Marrink SJ, Mark AE. 2003. Molecular dynamics simulation of the formation, structure, and dynamics of smallphospholipid vesicles. J Am Chem Soc 125:15233-15242.
Faller R, Marrink SJ. 2004. Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir 20:7686-7693.
Bennun SV, Longo, M., Faller R. Molecular scale structure in fluid-gel patterned bilayers: stability of interfacesand transmembrane distribution. To be submitted.
Bennun S, Longo ML, Faller R. 2007. The molecular scale structure in fluid-gel patterned bilayers: stability ofinterfaces and transmembrane distribution. Langmuir 23:12465-12468.
Brannigan G, Brown FLH. 2004. Solvent-free simulations of fluid membrane bilayers. J Chem Phys 120:1059-1071.
Noguchi H, Takasu M. 2001. Self-assembly of amphiphiles into vesicles: a Brownian dynamics simulation.Phys Rev E 64:041913.
Reynwar BJ, Illya G, Harmandaris VA, Müller MM, Kremer K, Deserno M. 2007. Aggregation and vesicula-tion of membrane proteins by curvature-mediated interactions. Nature 447:461-467.
Harmandaris VA, Deserno M. 2006. A novel method for measuring the bending rigidity of model lipid mem-branes by simulating tethers. J Chem Phys 125:204905.
Weeks JD, Chandler D, Andersen HC. 1971. Role of repulsive forces in determining the equilibrium structureof simple liquids. J Chem Phys 54:5237-5247.
Faller R, Kuhl TL. 2003. Modeling the binding of cholera-toxin to a lipid membrane by a non-additive two-dimensional hard disk model. Soft Mater 1:343-352.
Majewski J, Kuhl TL, Kjaer K, Smith GS. 2001. Packing of ganglioside-phospholipid monolayers: an x-raydiffraction and reflectivity study. Biophys J 81:2707-2715.
Humphrey W, Dalke A, Schulten K. 1996. VMD—visual molecular dynamics. J Mol Graphics 14:33-38.
Sayle RA, Milner-White EJ. 1995. RASMOL: biomolecular graphics for all. Trends Biochem Sci 20:374-376.
Pandit SA, Chiu S-W, Jakobsson E, Grama A, Scott HL. 2007. Cholesterol surrogates: a comparison of choles-terol and 16:0 ceramide in POPC bilayers. Biophys J 92:920-927.
Dickey AN, Faller R. 2007. How alcohol chain-length and concentration modulate hydrogen bond formation ina lipid bilayer. Biophys J 92:2366-2376.
Dickey AN, Faller R. 2005. Investigating interactions of biomembranes and alcohols: a multiscale approach. JPolym Sci B 43:1025-1032.
Kranenburg M, Venturoli M, Smit B. 2003. Phase behavior and induced interdigitation in bilayers studied withdissipative particle dynamics. J Phys Chem B 107:11491-11501.
Miller CE, Majewski J, Gog T, Kuhl TL. 2005. Characterization of biological thin films at the solid-liquid in-terface by x-ray reflectivity. Phys Rev Lett 94:238104.
Tieleman DP, Marrink SJ, Berendsen HJC. 1997. A computer perspective of membranes: molecular dynamicsstudies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270.
Davis JH. 1983. The description of membrane lipid conformation, order and dynamics by 2H-NMR. BiochimBiophys Acta 737:117-171.
Aittoniemi J, Róg T, Niemela P, Pasenkiewicz-Gierula M, Vattulainen I, Karttunen M. 2006. Sterol tilt: major determinant of sterol ordering capability in lipid membranes. J Phys Chem B Lett 110:25562-25564.
Lindahl E, Hess B, van der Spoel D. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306-317.
Luzar A, Chandler D. 1996. Hydrogen-bond kinetics in liquid water. Nature 379:55-57.
Ollila S, Hyvonen MT, Vattulainen I. 2007. Polyunsaturation in lipid membranes: dynamic properties and lat-eral pressure profiles. J Phys Chem B 111:3139-3150.
Chiu SW, Clark M, Balaji V, Subramaniam S, Scott HL, Jakobsson E. 1995. Incorporation of surface tensioninto molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys J 69:1230-1245.
Schmidt-Rohr K, Spiess HW. 1994. Multidimensional solid state NMR and polymers. New York: AcademicPress.
Dickey AN, Faller R. 2008. Behavioral differences between phosphatidic acid and phosphatidylcholine in the presence of the nicotinic acetylcholine receptor. Biophys J 95:2636-2646.
Dickey AN. 2008. How bilayer composition affects the stability of a model yeast membrane and the behavior of lipids surrounding the nicotinic acetylcholine receptor. PhD dissertation. University of California Davis.
Wong BY, Faller R. 2007. Phase behavior and dynamic heterogeneities in lipids: a coarse-grained simulation study of DPPC-DPPE mixtures. Biochim Biophys Acta 1768:620-627.
Sum AK, Faller R, de Pablo JJ. 2003. Molecular simulation study of phospholipid bilayers and insights of the interactions with disaccharides. Biophys J 85:2830-2844.
Patra M, Salonen E, Terama E, Vattulainen I, Faller R, Lee BW, Holopainen J, Karttunen M. 2006. Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers. Biophys J 90:1121-1135.
Crowe JH, Crowe LM, Carpenter JF, Rudolph AS, Wistrom CA, Spargo BJ, Anchordoguy TJ. 1988. Interac-tions of sugars with membranes. Biochim Biophys Acta 947:367-384.
Crowe JH, Crowe LM, Carpenter JF, Wistrom CA. 1987. Stabilization of dry phospholipid bilayers and pro-teins by sugar. Biochem J 242:1-10.
Crowe JH, Crowe LM, Oliver AE, Tsvetkova N, Wolkers W, Tablin F. 2001. The trehalose myth revisited: introduction to a symposium on stabilization of cells in the dry state. Cryobiology 43:89-105.
Crowe JH, Crowe LM, Chapman D. 1984. Preservation of membranes in anhydrobiotic organisms: the role of trehalose. Science 223:701-703.
Pereira CS, Lins RD, Chandrasekhar I, Carlos L, Freitas G, Hünenberger PH. 2004. Interaction of the disaccha-ride trehalose with a phospholipid bilayer: a molecular dynamics study. Biophys J 86:2273-2285.
Ly HV, Block DE, Longo ML. 2002. Interfacial tension effect of ethanol on lipid bilayer rigidity, stability, and area/molecule: a micropipet aspiration approach. Langmuir 18:8988-8995.
Ly HV, Longo ML. 2004. The influence of short-chain alcohols on interfacial tension, mechanical properties, area/molecule, and permeability of fluid lipid bilayers. Biophys J 87:1013-1033.
Bisson LF, Block DE. 2002. Ethanol tolerance in Saccharomyces. In Biodiversity and biotechnology of wine yeasts, pp. 85-98. Ed. M Ciani. Trivandrum, India: Research Signpost.
Cramer AC, Vlassides S, Block DE. 2002. Kinetic model for nitrogen-limited wine fermentations. Biotechnol Bioeng 77:49-60.
Bisson LF. 1999. Stuck and sluggish fermentations. Am J Enol Vitic 50:107-119.
Cantor RS. 1997. The lateral pressure profile in membranes: a physical mechanism of general anesthesia. Bio-chemistry 36:2339-2344.
Terama E, Ollila OH, Salonen E, Rowat AC, Trandum C, Westh P, Patra M, Karttunen M, Vattulainen I. 2008. Influence of ethanol on lipid membranes: from lateral pressure profiles to dynamics and partitioning. J Phys Chem B 112:4131-4139.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
2.1 Electronic Supplementary material
Figure 2.1.
Visualization of a POPA lipid bilayer [32]. Left: The system contains 128 lipids with 5443 water molecules. Middle: The POPA lipids without the water molecules. Right: Only the POPA headgroups are shown. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,842 KB)
Figure 2.2.
Electron density profiles of the POPA lipid bilayer from Figure 2.1. The bilayer center corresponds to a value of z = 0 nm. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,762 KB)
Figure 2.3.
An example of how the lipid acyl chains are numbered in calculating the order parameter. The POPA lipid shown here differs from the more commonly studied DPPC lipid in that the DPPC choline group is replaced with a hydrogen atom and the sn-2 tail contains a double bond and 18 atoms. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,772 KB)
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Dickey, A.N., Faller, R. (2010). Molecular Modeling of Biomembranes: A How-to Approach. In: Jue, T. (eds) Biomedical Applications of Biophysics. Handbook of Modern Biophysics, vol 3. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-233-9_2
Download citation
DOI: https://doi.org/10.1007/978-1-60327-233-9_2
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60327-232-2
Online ISBN: 978-1-60327-233-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)