Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid m...

Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent.

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performe...

Improving an all-atom force field.

Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve...

Systematic Assessment of the Effects of an All-Atom Force Field and the Implicit Solvent Model on the Refinement of NMR Structures with Subsets of Distance Restraints

Employment of a time consuming, sophisticated calculation using the all-atom force field and generalizedBorn implicit solvent model (GBIS) for refinement of NMR structures has become practical through advances in computational methods and capacities. GBIS refinement improves the qualities of the resulting NMR structures with reduced computational times. However, the contribution of GBIS to NMR ...

Coarse grained potential functions for proteins derived from all-atom explicit-solvent molecular dynamics simulations