Modifying the CHARMM36 Lipid Force Field for LJ-PME Simulations
نویسندگان
چکیده
منابع مشابه
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 in...
متن کامل4D geomechanical simulations for field development planning
3D and 4D geomechanical can be time-consuming to build and calibrate. However, once such a model is built, it is relative straightforward to use this model for various field development and management applications. In so doing, the return on the initial investment of time and effort in the creation of a 4D geomechanical model can be substantial. I present a case study where a 4D geomechanical m...
متن کاملLipid14: The Amber Lipid Force Field
The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail group...
متن کاملComparing simulations of lipid bilayers to scattering data: the GROMOS 43A1-S3 force field.
Simulations of DOPC at T = 303 K were performed using the united atom force field 43A1-S3 at six fixed projected areas, A(P) = 62, 64, 66, 68, 70, and 72 Å(2), as well as a tensionless simulation that produced an average A(NPT) = 65.8 Å(2). After a small undulation correction for the system size consisting of 288 lipids, results were compared to experimental data. The best, and excellent, fit t...
متن کاملThe MARTINI force field: coarse grained model for biomolecular simulations.
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction le...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2020
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2019.11.643