title: CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
abstract: 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 protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: Jumin
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Swails
authors.affiliation: Korean Institute of Science and Technology Information , Yuseong-gu, Daejeon 305-806, Korea.
authors.forename: Min Sun
authors.initials: MS
authors.lastname: Yeom
authors.affiliation: Department of Bioengineering, Stanford University , Stanford, California 94035, United States.
authors.forename: Peter K
authors.initials: PK
authors.lastname: Eastman
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Lemkul
authors.affiliation: Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Shuai
authors.initials: S
authors.lastname: Wei
authors.affiliation: Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Joshua
authors.initials: J
authors.lastname: Buckner
authors.affiliation: Cancer Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School , Boston, Massachusetts 02215, United States.
authors.forename: Jong Cheol
authors.initials: JC
authors.lastname: Jeong
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Qi
authors.affiliation: Leadership Computing Facility, Argonne National Laboratory , 9700 Cass Avenue, Building 240, Argonne, Illinois 60439, United States.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.affiliation: Department of Bioengineering, Stanford University , Stanford, California 94035, United States.
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States.
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.affiliation: Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
authors.affiliation: Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States.
authors.forename: Jeffery B
authors.initials: JB
authors.lastname: Klauda
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry; D010714:Phosphatidylethanolamines / Q000737:chemistry; D010718:Phosphatidylserines / Q000737:chemistry; D013109:Sphingomyelins / Q000737:chemistry
chemical_list: D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D010714:Phosphatidylethanolamines; D010718:Phosphatidylserines; D013109:Sphingomyelins; C033171:palmitoylsphingomyelin; C057561:1-palmitoyl-2-oleoylphosphatidylethanolamine; D015060:1,2-Dipalmitoylphosphatidylcholine; C050294:1-palmitoyl-2-oleoylglycero-3-phosphoserine; C017251:1,2-oleoylphosphatidylcholine