CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

• DOI: 10.1021/acs.jctc.5b00935
• Publication Date: 2015-11-12T23:08:34Z
• Authors: Jumin Lee; Xi Cheng; Jason M. Swails; Min Sun Yeom; Peter K. Eastman; Justin A. Lemkul; Shuai Wei; Joshua Buckner; Jong Cheol Jeong; Yifei Qi; Sunhwan Jo; Vijay S. Pande; David A. Case; Charles L. Brooks; Alexander D. MacK...; Jeffery B. Klauda; Wonpil Im
• Keywords: Force Field

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