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

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TitleCHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Publication TypeJournal Article
Year of Publication2016
AuthorsLee, J, Cheng, X, Swails, JM, Yeom, MSun, Eastman, PK, Lemkul, JA, Wei, S, Buckner, J, Jeong, JCheol, Qi, Y, Jo, S, Pande, VS, Case, DA, Brooks, CL, Mackerell, AD, Klauda, JB, Im, W
JournalJ Chem Theory Comput
Volume12
Issue1
Pagination405-13
Date Published2016 Jan 12
ISSN1549-9626
Keywords1,2-Dipalmitoylphosphatidylcholine, Lipid Bilayers, Molecular Dynamics Simulation, Phosphatidylcholines, Phosphatidylethanolamines, Phosphatidylserines, Sphingomyelins
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.

DOI10.1021/acs.jctc.5b00935
Alternate JournalJ Chem Theory Comput
PubMed ID26631602
PubMed Central IDPMC4712441
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM070855 / GM / NIGMS NIH HHS / United States
GM103695 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States
GM037554 / GM / NIGMS NIH HHS / United States
R01 GM103695 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States
F32GM109632 / GM / NIGMS NIH HHS / United States
F32 GM109632 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
U54GM087519 / GM / NIGMS NIH HHS / United States
R01GM072558 / GM / NIGMS NIH HHS / United States