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.
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.