First we briefly r eview Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe ...
Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes—exhaustively enumerating all 105 CG dimers—and across six phospholipids. For each combination, umbrella-sampling ...
Advanced ab initio molecular dynamics and coarse-grained molecular dynamics Kun Zhou, Bo Liu, in Molecular Dynamics Simulation, 2022 Abstract This chapter introduces two classes of advanced molecular dynamics (MD) methods: ab initio MD (AIMD) methods and coarse-grained MD (CGMD) methods. The AIMD...
Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein ...
However, our coarse-grained molecular dynamics simulation results showed that membrane tension can restrain polyarginine translocation across the asymmetric membrane and that this effect increases with increasing membrane tension. We also analyzed the structural properties and lipid topology of the tensed ...
A common way to perform simulations with a CG model is coarse-grained molecular dynamics (CGMD) simulations; like MD, they are based on the numerical integration of Newton's equation of motion with a suitable force field. In principle, the FF must be parameterized ad hoc for each system by...
A coarse-grained (CG) model of polyethylene glycol (PEG) was developed and implemented in CG molecular dynamics (MD) simulations of PEG chains with degree of polymerization (DP) 20 and 40. In the model, two repeat units of PEG are grouped as one CG bead. Atomistic MD simulation of PEG ...
molecular dynamicsphase behaviorPluronicSCFIn the framework of a hybrid particle-field simulation technique where self-consistent field (SCF) theory and molecular dynamics (MD) are combined, specific coarse-grained (CG) models for Pluronic block copolymers are developed. In particular, the behavior of...
The Coarse-Grained MD study based on TorchMD The coarse gain(CG) model implements the molecular dynamics simulation with simply the atom properties and interaction between them. Though lost certain de... P Xu,X Mou,Q Guo,... - 《Chinese Journal of Chemical Physics》 被引量: 0发表: 2021...
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with co...