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.
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
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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