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

Here we report that 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 wellmore » 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.« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [6] ;  [7] ;  [1] ;  [8] ;  [4] ;  [2] ;  [6] ;  [5] ;  [9] ;  [1]
  1. Univ. of Kansas, Lawrence, KS (United States). Dept. of Molecular Biosciences and Center for Computational Biology
  2. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
  3. Korean Inst. of Science and Technology Information, Daejeon (Korea)
  4. Stanford Univ., CA (United States). Dept. of Bioengineering
  5. Univ. of Maryland, College Park, MD (United States). Dept. of Pharmaceutical Sciences
  6. Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemistry
  7. Harvard Medical School, Boston, MA (United States). Cancer Research Inst.
  8. Argonne National Lab. (ANL), Argonne, IL (United States)
  9. Univ. of Maryland, College Park, MD (United States). Dept. of Chemical and Biomolecular Engineering
Publication Date:
OSTI Identifier:
1261132
Grant/Contract Number:
DBI-1145652; DBI-1145987; MCB-1149187; MCB-1157677; F32GM109632; GM037554; GM051501; GM070855; GM103695; R01GM072558; U54GM087519; KSC-2015-C3-004
Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Research Org:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE; National Science Foundation (NSF); National Inst. of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING