Optimal Simulation Protocols for Lipid Bilayers

To determine a set of optimal simulation protocols
for NAMD, GROMACS,
AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM C36
FF, a pure DPPC bilayer system was built and simulated with the various
simulation parameters available in each program. In addition, 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-sn-phosphatidylserine (POPS), and palmitoylsphingomyelin
(PSM) bilayer simulations were performed to validate the optimized
protocols derived from the DPPC simulations. The procedures of building
the lipid bilayer systems and the tested simulation parameters for
each program are provided in detail below.

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Lee J., Cheng X., Swails J.M., Yeom M.S., Eastman P.K., Lemkul J.A., Wei S., Buckner J., Jeong J.C., Qi Y., Jo S., Pande V.S., Case D.A., Brooks CL I.I.I., MacKerell AD J.r., Klauda J.B, & Im W. (2015). CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation, 12(1), 405-413.

Publication 2015

1 palmitoyl 2 oleoyl phosphatidylcholine Amber Dioleoyl phosphatidylcholine Lipid bilayer Palmitoylsphingomyelin Phosphatidylethanolamine Phosphatidylserine

Corresponding Organization :

Other organizations : University of Kansas, Rutgers, The State University of New Jersey, Korea Institute of Science & Technology Information, Stanford University, University of Maryland, Baltimore, Cancer Research Institute, Argonne National Laboratory, University of Michigan–Ann Arbor, Beth Israel Deaconess Medical Center, Harvard University, University of Maryland, College Park

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Variable analysis

independent variables

Simulation parameters available in each program (NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM)
Lipid bilayer systems (DPPC, DOPC, POPC, POPE, POPS, and PSM)

dependent variables

Optimal simulation protocols for the tested programs

control variables

CHARMM C36 force field used for all simulations

controls

The optimized protocols derived from the DPPC simulations were validated using the additional lipid bilayer systems (DOPC, POPC, POPE, POPS, and PSM)

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