CHARMM-GUI Input Generator for NAMD GROMACS AMBEROpenMM and CHARMM/OpenMM Simulations Using the CHARMM36 AdditiveForce Field

摘要

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocolused in CHARMM as well as from experiments. The optimal simulationprotocol was then applied to the other five lipid simulations andresulted in excellent agreement between results from most simulationprograms as well as with experimental data. AMBER compared least favorablywith the expected membrane properties, which appears to be due toits use of the hard-truncation in the LJ potential versus a force-basedswitching function used to smooth the LJ potential as it approachesthe cutoff distance. The optimal simulation protocol for each programhas been implemented in CHARMM-GUI. This protocol is expected to beapplicable to the remainder of the additive C36 FF including the proteins,nucleic acids, carbohydrates, and small molecules.