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

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…

• NS
  National Science Foundation

  Awards: MCB-1149187, 1145652, 1149187, DBI-1145652, 1157677, XSEDE MCB070009, 1145987, DBI-1145987, MCB070009, MCB-1157677
• KI
  Korea Institute of Science and Technology
• KI
  Korea Institute of Science and Technology Information

  Award: KSC-2015-C3-004
• NI
  National Institutes of Health

  Awards: GM037554, GM051501, GM070855, U54GM087519, GM103695, DBI-1145987, MCB-1157677, R01GM072558, NIH U54GM087519, F32GM109632, XSEDE MCB070009, MCB070009
• NI
  National Institute of General Medical Sciences

  Awards: GM037554, R01GM072558, GM070855, GM103695, F32GM109632, GM051501, U54GM087519
• DO
  Division of Molecular and Cellular Biosciences

  Awards: MCB-1157677, 1157677, 1149187, MCB-1149187
• DO
  Division of Biological Infrastructure

  Awards: DBI-1145652, DBI-1145987