Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions

2004 ◽  
Vol 108 (14) ◽  
pp. 4485-4494 ◽  
Author(s):  
Michael Patra ◽  
Mikko Karttunen ◽  
Marja T. Hyvönen ◽  
Emma Falck ◽  
Ilpo Vattulainen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Dynamics Simulations

Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

2009 ◽  
Vol 113 (10) ◽  
pp. 3112-3128 ◽  
Author(s):  
Maria M. Reif ◽  
Vincent Kräutler ◽  
Mika A. Kastenholz ◽  
Xavier Daura ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

2003 ◽  
Vol 50 (3) ◽  
pp. 789-798 ◽  
Author(s):  
Tomasz Róg ◽  
Krzysztof Murzyn ◽  
Marta Pasenkiewicz-Gierula
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Md Simulations ◽  
Computational Method ◽  
Simulation Protocol ◽  
Speed Up ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.

scholarly journals Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions

2003 ◽  
Vol 84 (6) ◽  
pp. 3636-3645 ◽  
Author(s):  
M. Patra ◽  
M. Karttunen ◽  
M.T. Hyvönen ◽  
E. Falck ◽  
P. Lindqvist ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Electrostatic Interactions ◽  
Dynamics Simulations
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